Starting phenix.real_space_refine on Thu Jan 18 19:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m20_23627/01_2024/7m20_23627_updated.pdb" } resolution = 3.84 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= 0.018 sd= 0.504 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: 6 Type Number sf(0) Gaussians P 45 5.49 5 S 405 5.16 5 Cl 9 4.86 5 C 38223 2.51 5 N 10278 2.21 5 O 11745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F ARG 391": "NH1" <-> "NH2" Residue "F GLU 407": "OE1" <-> "OE2" Residue "E GLU 423": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ARG 391": "NH1" <-> "NH2" Residue "H GLU 407": "OE1" <-> "OE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "G GLU 434": "OE1" <-> "OE2" Residue "J GLU 125": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J GLU 198": "OE1" <-> "OE2" Residue "J ARG 391": "NH1" <-> "NH2" Residue "J GLU 407": "OE1" <-> "OE2" Residue "I GLU 423": "OE1" <-> "OE2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 158": "OE1" <-> "OE2" Residue "L GLU 198": "OE1" <-> "OE2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "L GLU 407": "OE1" <-> "OE2" Residue "K GLU 423": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "N GLU 125": "OE1" <-> "OE2" Residue "N GLU 158": "OE1" <-> "OE2" Residue "N GLU 198": "OE1" <-> "OE2" Residue "N ARG 391": "NH1" <-> "NH2" Residue "N GLU 407": "OE1" <-> "OE2" Residue "M GLU 423": "OE1" <-> "OE2" Residue "M GLU 434": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 198": "OE1" <-> "OE2" Residue "P ARG 391": "NH1" <-> "NH2" Residue "P GLU 407": "OE1" <-> "OE2" Residue "O GLU 423": "OE1" <-> "OE2" Residue "O GLU 434": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 158": "OE1" <-> "OE2" Residue "R GLU 198": "OE1" <-> "OE2" Residue "R ARG 391": "NH1" <-> "NH2" Residue "R GLU 407": "OE1" <-> "OE2" Residue "Q GLU 423": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 60705 Number of models: 1 Model: "" Number of chains: 36 Chain: "B" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "N" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "P" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "O" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "R" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3314 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Q" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3325 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 415} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 74 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'GTP': 1, 'YNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5957 SG CYS A 347 255.861 256.642 23.515 1.00168.57 S ATOM 12596 SG CYS C 347 178.738 294.451 23.515 1.00168.57 S ATOM 19235 SG CYS E 347 95.356 273.841 23.515 1.00168.57 S ATOM 25874 SG CYS G 347 44.729 204.455 23.515 1.00168.57 S ATOM 32513 SG CYS I 347 50.547 118.760 23.515 1.00168.57 S ATOM 39152 SG CYS K 347 110.087 56.854 23.515 1.00168.57 S ATOM 45791 SG CYS M 347 195.490 47.703 23.515 1.00168.57 S ATOM 52430 SG CYS O 347 266.795 95.589 23.515 1.00168.57 S ATOM 59069 SG CYS Q 347 290.637 178.105 23.515 1.00168.57 S Time building chain proxies: 23.72, per 1000 atoms: 0.39 Number of scatterers: 60705 At special positions: 0 Unit cell: (336.02, 334.96, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 9 17.00 S 405 16.00 P 45 15.00 O 11745 8.00 N 10278 7.00 C 38223 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: 20.29 Conformation dependent library (CDL) restraints added in 8.5 seconds 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 306 helices and 45 sheets defined 42.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.12 Creating SS restraints... Processing helix chain 'B' and resid 12 through 28 Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.097A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 372 through 390 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 105 through 108 No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.356A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 183 through 193 removed outlier: 4.538A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.761A pdb=" N LYS A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET D 73 " --> pdb=" O PRO D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.096A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 222 through 241 removed outlier: 3.841A pdb=" N ASN D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.231A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 372 through 390 Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 406 through 425 Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 74 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 105 through 108 No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 111 through 128 removed outlier: 4.356A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 183 through 193 removed outlier: 4.538A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.205A pdb=" N THR C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.761A pdb=" N LYS C 336 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 399 Processing helix chain 'C' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 Processing helix chain 'F' and resid 12 through 28 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET F 73 " --> pdb=" O PRO F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 181 through 195 removed outlier: 4.096A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN F 226 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 372 through 390 Processing helix chain 'F' and resid 395 through 401 Processing helix chain 'F' and resid 406 through 425 Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 105 through 108 No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 111 through 128 removed outlier: 4.357A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 183 through 193 removed outlier: 4.538A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.761A pdb=" N LYS E 336 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 399 Processing helix chain 'E' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 Processing helix chain 'H' and resid 12 through 28 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 158 Processing helix chain 'H' and resid 181 through 195 removed outlier: 4.096A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN H 226 " --> pdb=" O TYR H 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 336 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 372 through 390 Processing helix chain 'H' and resid 395 through 401 Processing helix chain 'H' and resid 406 through 425 Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU G 22 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU G 23 " --> pdb=" O ALA G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 74 through 80 Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 105 through 108 No H-bonds generated for 'chain 'G' and resid 105 through 108' Processing helix chain 'G' and resid 111 through 128 removed outlier: 4.357A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 160 Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 183 through 193 removed outlier: 4.539A pdb=" N THR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 288 through 293 removed outlier: 4.205A pdb=" N THR G 292 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 337 removed outlier: 3.762A pdb=" N LYS G 336 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR G 337 " --> pdb=" O ALA G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 399 Processing helix chain 'G' and resid 405 through 411 removed outlier: 5.319A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 434 Processing helix chain 'J' and resid 12 through 28 Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 70 through 77 removed outlier: 3.553A pdb=" N MET J 73 " --> pdb=" O PRO J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 4.276A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 181 through 195 removed outlier: 4.097A pdb=" N GLN J 191 " --> pdb=" O LEU J 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU J 194 " --> pdb=" O HIS J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 222 through 241 removed outlier: 3.841A pdb=" N ASN J 226 " --> pdb=" O TYR J 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER J 239 " --> pdb=" O GLY J 235 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU J 240 " --> pdb=" O VAL J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 257 Processing helix chain 'J' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE J 294 " --> pdb=" O THR J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 336 Processing helix chain 'J' and resid 338 through 340 No H-bonds generated for 'chain 'J' and resid 338 through 340' Processing helix chain 'J' and resid 372 through 390 Processing helix chain 'J' and resid 395 through 401 Processing helix chain 'J' and resid 406 through 425 Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.715A pdb=" N GLU I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 74 through 80 Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 105 through 108 No H-bonds generated for 'chain 'I' and resid 105 through 108' Processing helix chain 'I' and resid 111 through 128 removed outlier: 4.356A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 160 Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 183 through 193 removed outlier: 4.539A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR I 292 " --> pdb=" O VAL I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 337 removed outlier: 3.761A pdb=" N LYS I 336 " --> pdb=" O ILE I 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR I 337 " --> pdb=" O ALA I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 399 Processing helix chain 'I' and resid 405 through 411 removed outlier: 5.319A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 434 Processing helix chain 'L' and resid 12 through 28 Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET L 73 " --> pdb=" O PRO L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 158 Processing helix chain 'L' and resid 181 through 195 removed outlier: 4.097A pdb=" N GLN L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 213 Processing helix chain 'L' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN L 226 " --> pdb=" O TYR L 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER L 239 " --> pdb=" O GLY L 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU L 240 " --> pdb=" O VAL L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 257 Processing helix chain 'L' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE L 294 " --> pdb=" O THR L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 336 Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 372 through 390 Processing helix chain 'L' and resid 395 through 401 Processing helix chain 'L' and resid 406 through 425 Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 74 through 80 Processing helix chain 'K' and resid 82 through 86 Processing helix chain 'K' and resid 105 through 108 No H-bonds generated for 'chain 'K' and resid 105 through 108' Processing helix chain 'K' and resid 111 through 128 removed outlier: 4.356A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 160 Processing helix chain 'K' and resid 175 through 177 No H-bonds generated for 'chain 'K' and resid 175 through 177' Processing helix chain 'K' and resid 183 through 193 removed outlier: 4.539A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR K 292 " --> pdb=" O VAL K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 removed outlier: 3.762A pdb=" N LYS K 336 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR K 337 " --> pdb=" O ALA K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 399 Processing helix chain 'K' and resid 405 through 411 removed outlier: 5.319A pdb=" N GLU K 411 " --> pdb=" O TRP K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 434 Processing helix chain 'N' and resid 12 through 28 Processing helix chain 'N' and resid 41 through 44 No H-bonds generated for 'chain 'N' and resid 41 through 44' Processing helix chain 'N' and resid 47 through 49 No H-bonds generated for 'chain 'N' and resid 47 through 49' Processing helix chain 'N' and resid 70 through 77 removed outlier: 3.553A pdb=" N MET N 73 " --> pdb=" O PRO N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 158 Processing helix chain 'N' and resid 181 through 195 removed outlier: 4.095A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 213 Processing helix chain 'N' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN N 226 " --> pdb=" O TYR N 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER N 239 " --> pdb=" O GLY N 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU N 240 " --> pdb=" O VAL N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 257 Processing helix chain 'N' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE N 294 " --> pdb=" O THR N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 336 Processing helix chain 'N' and resid 338 through 340 No H-bonds generated for 'chain 'N' and resid 338 through 340' Processing helix chain 'N' and resid 372 through 390 Processing helix chain 'N' and resid 395 through 401 Processing helix chain 'N' and resid 406 through 425 Processing helix chain 'M' and resid 10 through 27 removed outlier: 3.717A pdb=" N GLU M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 74 through 80 Processing helix chain 'M' and resid 82 through 86 Processing helix chain 'M' and resid 105 through 108 No H-bonds generated for 'chain 'M' and resid 105 through 108' Processing helix chain 'M' and resid 111 through 128 removed outlier: 4.357A pdb=" N ASP M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN M 128 " --> pdb=" O LYS M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 160 Processing helix chain 'M' and resid 175 through 177 No H-bonds generated for 'chain 'M' and resid 175 through 177' Processing helix chain 'M' and resid 183 through 193 removed outlier: 4.538A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 216 Processing helix chain 'M' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU M 242 " --> pdb=" O ILE M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 259 Processing helix chain 'M' and resid 288 through 293 removed outlier: 4.205A pdb=" N THR M 292 " --> pdb=" O VAL M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 309 No H-bonds generated for 'chain 'M' and resid 307 through 309' Processing helix chain 'M' and resid 325 through 337 removed outlier: 3.761A pdb=" N LYS M 336 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR M 337 " --> pdb=" O ALA M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 399 Processing helix chain 'M' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU M 411 " --> pdb=" O TRP M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 434 Processing helix chain 'P' and resid 12 through 28 Processing helix chain 'P' and resid 41 through 44 No H-bonds generated for 'chain 'P' and resid 41 through 44' Processing helix chain 'P' and resid 47 through 49 No H-bonds generated for 'chain 'P' and resid 47 through 49' Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.552A pdb=" N MET P 73 " --> pdb=" O PRO P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER P 115 " --> pdb=" O GLU P 111 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN P 126 " --> pdb=" O LYS P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 158 Processing helix chain 'P' and resid 181 through 195 removed outlier: 4.096A pdb=" N GLN P 191 " --> pdb=" O LEU P 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU P 194 " --> pdb=" O HIS P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 213 Processing helix chain 'P' and resid 222 through 241 removed outlier: 3.840A pdb=" N ASN P 226 " --> pdb=" O TYR P 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER P 239 " --> pdb=" O GLY P 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU P 240 " --> pdb=" O VAL P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 257 Processing helix chain 'P' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE P 294 " --> pdb=" O THR P 290 " (cutoff:3.500A) Processing helix chain 'P' and resid 323 through 336 Processing helix chain 'P' and resid 338 through 340 No H-bonds generated for 'chain 'P' and resid 338 through 340' Processing helix chain 'P' and resid 372 through 390 Processing helix chain 'P' and resid 395 through 401 Processing helix chain 'P' and resid 406 through 425 Processing helix chain 'O' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU O 22 " --> pdb=" O ASN O 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU O 23 " --> pdb=" O ALA O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 52 No H-bonds generated for 'chain 'O' and resid 50 through 52' Processing helix chain 'O' and resid 74 through 80 Processing helix chain 'O' and resid 82 through 86 Processing helix chain 'O' and resid 105 through 108 No H-bonds generated for 'chain 'O' and resid 105 through 108' Processing helix chain 'O' and resid 111 through 128 removed outlier: 4.357A pdb=" N ASP O 116 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU O 117 " --> pdb=" O GLU O 113 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN O 128 " --> pdb=" O LYS O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 160 Processing helix chain 'O' and resid 175 through 177 No H-bonds generated for 'chain 'O' and resid 175 through 177' Processing helix chain 'O' and resid 183 through 193 removed outlier: 4.538A pdb=" N THR O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 216 Processing helix chain 'O' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU O 242 " --> pdb=" O ILE O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR O 292 " --> pdb=" O VAL O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 309 No H-bonds generated for 'chain 'O' and resid 307 through 309' Processing helix chain 'O' and resid 325 through 337 removed outlier: 3.762A pdb=" N LYS O 336 " --> pdb=" O ILE O 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR O 337 " --> pdb=" O ALA O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 399 Processing helix chain 'O' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU O 411 " --> pdb=" O TRP O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 416 through 434 Processing helix chain 'R' and resid 12 through 28 Processing helix chain 'R' and resid 41 through 44 No H-bonds generated for 'chain 'R' and resid 41 through 44' Processing helix chain 'R' and resid 47 through 49 No H-bonds generated for 'chain 'R' and resid 47 through 49' Processing helix chain 'R' and resid 70 through 77 removed outlier: 3.553A pdb=" N MET R 73 " --> pdb=" O PRO R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 126 removed outlier: 4.275A pdb=" N ASP R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 158 Processing helix chain 'R' and resid 181 through 195 removed outlier: 4.096A pdb=" N GLN R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLU R 194 " --> pdb=" O HIS R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 213 Processing helix chain 'R' and resid 222 through 241 removed outlier: 3.841A pdb=" N ASN R 226 " --> pdb=" O TYR R 222 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER R 239 " --> pdb=" O GLY R 235 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU R 240 " --> pdb=" O VAL R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 257 Processing helix chain 'R' and resid 286 through 294 removed outlier: 4.230A pdb=" N PHE R 294 " --> pdb=" O THR R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 336 Processing helix chain 'R' and resid 338 through 340 No H-bonds generated for 'chain 'R' and resid 338 through 340' Processing helix chain 'R' and resid 372 through 390 Processing helix chain 'R' and resid 395 through 401 Processing helix chain 'R' and resid 406 through 425 Processing helix chain 'Q' and resid 10 through 27 removed outlier: 3.716A pdb=" N GLU Q 22 " --> pdb=" O ASN Q 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 74 through 80 Processing helix chain 'Q' and resid 82 through 86 Processing helix chain 'Q' and resid 105 through 108 No H-bonds generated for 'chain 'Q' and resid 105 through 108' Processing helix chain 'Q' and resid 111 through 128 removed outlier: 4.356A pdb=" N ASP Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 148 through 160 Processing helix chain 'Q' and resid 175 through 177 No H-bonds generated for 'chain 'Q' and resid 175 through 177' Processing helix chain 'Q' and resid 183 through 193 removed outlier: 4.537A pdb=" N THR Q 193 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 216 Processing helix chain 'Q' and resid 227 through 244 removed outlier: 4.583A pdb=" N SER Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU Q 242 " --> pdb=" O ILE Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 259 Processing helix chain 'Q' and resid 288 through 293 removed outlier: 4.206A pdb=" N THR Q 292 " --> pdb=" O VAL Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 325 through 337 removed outlier: 3.762A pdb=" N LYS Q 336 " --> pdb=" O ILE Q 332 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR Q 337 " --> pdb=" O ALA Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 399 Processing helix chain 'Q' and resid 405 through 411 removed outlier: 5.320A pdb=" N GLU Q 411 " --> pdb=" O TRP Q 407 " (cutoff:3.500A) Processing helix chain 'Q' and resid 416 through 434 Processing sheet with id= A, first strand: chain 'B' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL B 170 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 350 through 354 removed outlier: 3.654A pdb=" N ALA B 352 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N THR B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR B 366 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.240A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 63 through 65 removed outlier: 8.266A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 51 through 53 Processing sheet with id= H, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL D 170 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 350 through 354 removed outlier: 3.653A pdb=" N ALA D 352 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR D 366 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 65 through 68 removed outlier: 7.240A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 63 through 65 removed outlier: 8.266A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 163 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU F 135 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 51 through 53 Processing sheet with id= M, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.633A pdb=" N VAL F 170 " --> pdb=" O ILE F 202 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 350 through 354 removed outlier: 3.653A pdb=" N ALA F 352 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN F 370 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL F 313 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE F 368 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR F 315 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR F 366 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.240A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 63 through 65 removed outlier: 8.266A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 163 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU H 135 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 51 through 53 Processing sheet with id= R, first strand: chain 'H' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL H 170 " --> pdb=" O ILE H 202 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 350 through 354 removed outlier: 3.654A pdb=" N ALA H 352 " --> pdb=" O THR H 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN H 370 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL H 313 " --> pdb=" O ILE H 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE H 368 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N THR H 315 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR H 366 " --> pdb=" O THR H 315 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 65 through 68 removed outlier: 7.239A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER G 140 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS G 139 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS G 200 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER G 170 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR G 172 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL G 204 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE J 64 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS J 6 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL J 5 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE J 133 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE J 7 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU J 135 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE J 163 " --> pdb=" O PHE J 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU J 135 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN J 165 " --> pdb=" O LEU J 135 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 51 through 53 Processing sheet with id= W, first strand: chain 'J' and resid 168 through 170 removed outlier: 3.635A pdb=" N VAL J 170 " --> pdb=" O ILE J 202 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 350 through 354 removed outlier: 3.654A pdb=" N ALA J 352 " --> pdb=" O THR J 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN J 370 " --> pdb=" O LEU J 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL J 313 " --> pdb=" O ILE J 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE J 368 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR J 315 " --> pdb=" O THR J 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR J 366 " --> pdb=" O THR J 315 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 65 through 68 removed outlier: 7.239A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER I 140 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS I 139 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR I 172 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL I 204 " --> pdb=" O TYR I 172 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE L 64 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS L 6 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL L 5 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE L 133 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE L 7 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU L 135 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE L 163 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU L 135 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN L 165 " --> pdb=" O LEU L 135 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 51 through 53 Processing sheet with id= AB, first strand: chain 'L' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL L 170 " --> pdb=" O ILE L 202 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 350 through 354 removed outlier: 3.654A pdb=" N ALA L 352 " --> pdb=" O THR L 315 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN L 370 " --> pdb=" O LEU L 311 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL L 313 " --> pdb=" O ILE L 368 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE L 368 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR L 315 " --> pdb=" O THR L 366 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR L 366 " --> pdb=" O THR L 315 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 65 through 68 removed outlier: 7.239A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'N' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE N 64 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS N 6 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL N 5 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE N 133 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE N 7 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU N 135 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE N 163 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU N 135 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN N 165 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'N' and resid 51 through 53 Processing sheet with id= AG, first strand: chain 'N' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL N 170 " --> pdb=" O ILE N 202 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 350 through 354 removed outlier: 3.654A pdb=" N ALA N 352 " --> pdb=" O THR N 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN N 370 " --> pdb=" O LEU N 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL N 313 " --> pdb=" O ILE N 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE N 368 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR N 315 " --> pdb=" O THR N 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR N 366 " --> pdb=" O THR N 315 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 65 through 68 removed outlier: 7.239A pdb=" N SER M 6 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL M 68 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS M 8 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER M 140 " --> pdb=" O VAL M 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU M 167 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS M 139 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE M 169 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS M 200 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER M 170 " --> pdb=" O CYS M 200 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE M 202 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR M 172 " --> pdb=" O PHE M 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL M 204 " --> pdb=" O TYR M 172 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'P' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE P 64 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS P 6 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL P 5 " --> pdb=" O GLN P 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE P 133 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE P 7 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU P 135 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE P 163 " --> pdb=" O PHE P 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU P 135 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN P 165 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 51 through 53 Processing sheet with id= AL, first strand: chain 'P' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL P 170 " --> pdb=" O ILE P 202 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'P' and resid 350 through 354 removed outlier: 3.653A pdb=" N ALA P 352 " --> pdb=" O THR P 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN P 370 " --> pdb=" O LEU P 311 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL P 313 " --> pdb=" O ILE P 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE P 368 " --> pdb=" O VAL P 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR P 315 " --> pdb=" O THR P 366 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR P 366 " --> pdb=" O THR P 315 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 65 through 68 removed outlier: 7.240A pdb=" N SER O 6 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL O 68 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS O 8 " --> pdb=" O VAL O 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER O 140 " --> pdb=" O VAL O 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU O 167 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS O 139 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE O 169 " --> pdb=" O HIS O 139 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS O 200 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER O 170 " --> pdb=" O CYS O 200 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N PHE O 202 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR O 172 " --> pdb=" O PHE O 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL O 204 " --> pdb=" O TYR O 172 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'R' and resid 63 through 65 removed outlier: 8.267A pdb=" N ILE R 64 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS R 6 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL R 5 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE R 133 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE R 7 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU R 135 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE R 163 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N LEU R 135 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN R 165 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'R' and resid 168 through 170 removed outlier: 3.634A pdb=" N VAL R 170 " --> pdb=" O ILE R 202 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'R' and resid 350 through 354 removed outlier: 3.653A pdb=" N ALA R 352 " --> pdb=" O THR R 315 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN R 370 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL R 313 " --> pdb=" O ILE R 368 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE R 368 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR R 315 " --> pdb=" O THR R 366 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR R 366 " --> pdb=" O THR R 315 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 65 through 68 removed outlier: 7.239A pdb=" N SER Q 6 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL Q 68 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS Q 8 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER Q 140 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU Q 167 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS Q 139 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE Q 169 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS Q 200 " --> pdb=" O GLU Q 168 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER Q 170 " --> pdb=" O CYS Q 200 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE Q 202 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR Q 172 " --> pdb=" O PHE Q 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL Q 204 " --> pdb=" O TYR Q 172 " (cutoff:3.500A) 2106 hydrogen bonds defined for protein. 4914 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: 18.23 Time building geometry restraints manager: 21.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10242 1.31 - 1.44: 16785 1.44 - 1.56: 34353 1.56 - 1.69: 81 1.69 - 1.81: 639 Bond restraints: 62100 Sorted by residual: bond pdb=" C7 YNP K 501 " pdb=" C8 YNP K 501 " ideal model delta sigma weight residual 1.579 1.326 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C7 YNP A 501 " pdb=" C8 YNP A 501 " ideal model delta sigma weight residual 1.579 1.326 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C7 YNP E 501 " pdb=" C8 YNP E 501 " ideal model delta sigma weight residual 1.579 1.327 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C7 YNP G 501 " pdb=" C8 YNP G 501 " ideal model delta sigma weight residual 1.579 1.327 0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C7 YNP Q 501 " pdb=" C8 YNP Q 501 " ideal model delta sigma weight residual 1.579 1.327 0.252 2.00e-02 2.50e+03 1.59e+02 ... (remaining 62095 not shown) Histogram of bond angle deviations from ideal: 53.06 - 76.54: 27 76.54 - 100.02: 45 100.02 - 123.50: 82375 123.50 - 146.97: 2054 146.97 - 170.45: 27 Bond angle restraints: 84528 Sorted by residual: angle pdb=" C3 YNP O 501 " pdb=" N1 YNP O 501 " pdb=" C4 YNP O 501 " ideal model delta sigma weight residual 109.66 170.45 -60.79 3.00e+00 1.11e-01 4.11e+02 angle pdb=" C3 YNP C 501 " pdb=" N1 YNP C 501 " pdb=" C4 YNP C 501 " ideal model delta sigma weight residual 109.66 170.28 -60.62 3.00e+00 1.11e-01 4.08e+02 angle pdb=" C3 YNP G 501 " pdb=" N1 YNP G 501 " pdb=" C4 YNP G 501 " ideal model delta sigma weight residual 109.66 170.24 -60.58 3.00e+00 1.11e-01 4.08e+02 angle pdb=" C3 YNP E 501 " pdb=" N1 YNP E 501 " pdb=" C4 YNP E 501 " ideal model delta sigma weight residual 109.66 170.22 -60.56 3.00e+00 1.11e-01 4.08e+02 angle pdb=" C3 YNP M 501 " pdb=" N1 YNP M 501 " pdb=" C4 YNP M 501 " ideal model delta sigma weight residual 109.66 170.22 -60.56 3.00e+00 1.11e-01 4.08e+02 ... (remaining 84523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 35750 35.57 - 71.15: 869 71.15 - 106.72: 246 106.72 - 142.30: 35 142.30 - 177.87: 99 Dihedral angle restraints: 36999 sinusoidal: 14544 harmonic: 22455 Sorted by residual: dihedral pdb=" C4' GTP K 502 " pdb=" C5' GTP K 502 " pdb=" O5' GTP K 502 " pdb=" PA GTP K 502 " ideal model delta sinusoidal sigma weight residual -99.13 76.29 -175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP C 502 " pdb=" C5' GTP C 502 " pdb=" O5' GTP C 502 " pdb=" PA GTP C 502 " ideal model delta sinusoidal sigma weight residual -99.13 76.29 -175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C4' GTP Q 502 " pdb=" C5' GTP Q 502 " pdb=" O5' GTP Q 502 " pdb=" PA GTP Q 502 " ideal model delta sinusoidal sigma weight residual -99.13 76.29 -175.42 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 36996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 8125 0.093 - 0.185: 975 0.185 - 0.278: 197 0.278 - 0.370: 21 0.370 - 0.463: 24 Chirality restraints: 9342 Sorted by residual: chirality pdb=" CG LEU P 225 " pdb=" CB LEU P 225 " pdb=" CD1 LEU P 225 " pdb=" CD2 LEU P 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CG LEU F 225 " pdb=" CB LEU F 225 " pdb=" CD1 LEU F 225 " pdb=" CD2 LEU F 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" CG LEU J 225 " pdb=" CB LEU J 225 " pdb=" CD1 LEU J 225 " pdb=" CD2 LEU J 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 9339 not shown) Planarity restraints: 10989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 YNP G 501 " -0.125 2.00e-02 2.50e+03 1.11e-01 1.53e+02 pdb=" C6 YNP G 501 " 0.037 2.00e-02 2.50e+03 pdb=" C7 YNP G 501 " -0.035 2.00e-02 2.50e+03 pdb=" N2 YNP G 501 " 0.194 2.00e-02 2.50e+03 pdb=" O2 YNP G 501 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 YNP K 501 " -0.125 2.00e-02 2.50e+03 1.10e-01 1.52e+02 pdb=" C6 YNP K 501 " 0.037 2.00e-02 2.50e+03 pdb=" C7 YNP K 501 " -0.035 2.00e-02 2.50e+03 pdb=" N2 YNP K 501 " 0.194 2.00e-02 2.50e+03 pdb=" O2 YNP K 501 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 YNP E 501 " -0.125 2.00e-02 2.50e+03 1.10e-01 1.52e+02 pdb=" C6 YNP E 501 " 0.037 2.00e-02 2.50e+03 pdb=" C7 YNP E 501 " -0.035 2.00e-02 2.50e+03 pdb=" N2 YNP E 501 " 0.194 2.00e-02 2.50e+03 pdb=" O2 YNP E 501 " -0.071 2.00e-02 2.50e+03 ... (remaining 10986 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3495 2.70 - 3.25: 69426 3.25 - 3.80: 101610 3.80 - 4.35: 126372 4.35 - 4.90: 197287 Nonbonded interactions: 498190 Sorted by model distance: nonbonded pdb=" SG CYS H 129 " pdb=" OE2 GLU I 97 " model vdw 2.148 3.400 nonbonded pdb=" OE2 GLU A 97 " pdb=" SG CYS R 129 " model vdw 2.148 3.400 nonbonded pdb=" SG CYS D 129 " pdb=" OE2 GLU E 97 " model vdw 2.148 3.400 nonbonded pdb=" SG CYS B 129 " pdb=" OE2 GLU C 97 " model vdw 2.148 3.400 nonbonded pdb=" SG CYS P 129 " pdb=" OE2 GLU Q 97 " model vdw 2.148 3.400 ... (remaining 498185 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 40.870 Check model and map are aligned: 0.740 Set scattering table: 0.430 Process input model: 124.390 Find NCS groups from input model: 3.660 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.009 0.253 62100 Z= 0.634 Angle : 1.556 60.791 84528 Z= 0.773 Chirality : 0.071 0.463 9342 Planarity : 0.007 0.111 10989 Dihedral : 20.405 177.873 22599 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 30.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.06 % Favored : 88.59 % Rotamer: Outliers : 2.84 % Allowed : 3.75 % Favored : 93.41 % 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: -2.43 (0.09), residues: 7749 helix: -0.52 (0.09), residues: 3204 sheet: -1.66 (0.15), residues: 1062 loop : -2.65 (0.10), residues: 3483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP D 101 HIS 0.009 0.002 HIS J 227 PHE 0.023 0.002 PHE Q 255 TYR 0.022 0.003 TYR G 224 ARG 0.011 0.001 ARG I 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1321 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 ARG cc_start: 0.6983 (mtp180) cc_final: 0.6607 (ttm-80) REVERT: B 325 GLU cc_start: 0.8410 (pp20) cc_final: 0.8205 (pp20) REVERT: B 361 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6692 (mt) REVERT: B 406 MET cc_start: 0.8755 (mmp) cc_final: 0.8554 (mmp) REVERT: A 214 ARG cc_start: 0.6239 (tmm160) cc_final: 0.5365 (tpp80) REVERT: A 425 MET cc_start: 0.8695 (mmt) cc_final: 0.8476 (mmt) REVERT: D 14 ASN cc_start: 0.8319 (m-40) cc_final: 0.7822 (m110) REVERT: D 205 GLU cc_start: 0.9445 (tt0) cc_final: 0.9233 (tt0) REVERT: D 282 ARG cc_start: 0.7087 (mtp180) cc_final: 0.6870 (mtp85) REVERT: D 325 GLU cc_start: 0.8358 (pp20) cc_final: 0.8147 (pp20) REVERT: D 361 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6503 (mm) REVERT: D 406 MET cc_start: 0.8670 (mmp) cc_final: 0.8347 (mmp) REVERT: C 214 ARG cc_start: 0.6250 (tmm160) cc_final: 0.5547 (tpp80) REVERT: C 227 LEU cc_start: 0.8696 (mm) cc_final: 0.8473 (mm) REVERT: C 313 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7223 (mmm) REVERT: C 317 LEU cc_start: 0.8409 (mt) cc_final: 0.8187 (mt) REVERT: C 377 MET cc_start: 0.7410 (mtt) cc_final: 0.7187 (mtp) REVERT: F 167 PHE cc_start: 0.6795 (m-80) cc_final: 0.6434 (m-80) REVERT: F 282 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6587 (ttm-80) REVERT: F 361 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6902 (mt) REVERT: F 406 MET cc_start: 0.8747 (mmp) cc_final: 0.8538 (mmp) REVERT: E 214 ARG cc_start: 0.6060 (tmm160) cc_final: 0.5079 (tpp80) REVERT: E 393 HIS cc_start: 0.8021 (m90) cc_final: 0.7780 (t70) REVERT: E 425 MET cc_start: 0.8777 (mmt) cc_final: 0.8556 (mmm) REVERT: H 91 ILE cc_start: 0.8887 (tt) cc_final: 0.8686 (mm) REVERT: H 282 ARG cc_start: 0.7025 (mtp180) cc_final: 0.6718 (mtp85) REVERT: H 325 GLU cc_start: 0.8274 (pp20) cc_final: 0.7919 (pp20) REVERT: H 361 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7065 (mt) REVERT: H 388 MET cc_start: 0.8483 (ttm) cc_final: 0.8179 (ttp) REVERT: G 214 ARG cc_start: 0.5996 (tmm160) cc_final: 0.5292 (tpp80) REVERT: G 227 LEU cc_start: 0.8694 (mm) cc_final: 0.8451 (mm) REVERT: G 377 MET cc_start: 0.7265 (mtt) cc_final: 0.7025 (mtp) REVERT: J 257 MET cc_start: 0.9272 (mmp) cc_final: 0.8985 (mmp) REVERT: J 282 ARG cc_start: 0.7043 (mtp180) cc_final: 0.6401 (ttm-80) REVERT: J 284 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7782 (mp) REVERT: J 309 ARG cc_start: 0.5433 (mtt-85) cc_final: 0.5201 (mtt-85) REVERT: J 361 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6845 (mt) REVERT: J 363 MET cc_start: 0.3351 (ptt) cc_final: 0.2819 (ptt) REVERT: J 388 MET cc_start: 0.8427 (ttm) cc_final: 0.7907 (ttm) REVERT: J 406 MET cc_start: 0.8733 (mmp) cc_final: 0.8531 (mmp) REVERT: I 189 LEU cc_start: 0.9503 (tp) cc_final: 0.9261 (tp) REVERT: I 214 ARG cc_start: 0.6234 (tmm160) cc_final: 0.5021 (tpp80) REVERT: I 227 LEU cc_start: 0.8692 (mm) cc_final: 0.8447 (mm) REVERT: L 361 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6442 (mm) REVERT: K 214 ARG cc_start: 0.6399 (tmm160) cc_final: 0.5532 (tpp80) REVERT: K 227 LEU cc_start: 0.8714 (mm) cc_final: 0.8481 (mm) REVERT: K 233 GLN cc_start: 0.9118 (tp40) cc_final: 0.8055 (tm-30) REVERT: K 425 MET cc_start: 0.8711 (mmt) cc_final: 0.8178 (mmt) REVERT: N 257 MET cc_start: 0.9289 (mmp) cc_final: 0.9087 (mmp) REVERT: N 282 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6640 (mtp85) REVERT: N 325 GLU cc_start: 0.8399 (pp20) cc_final: 0.8168 (pp20) REVERT: N 361 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6968 (mt) REVERT: M 214 ARG cc_start: 0.6484 (tmm160) cc_final: 0.5634 (tpp80) REVERT: M 227 LEU cc_start: 0.8550 (mm) cc_final: 0.8281 (mm) REVERT: M 377 MET cc_start: 0.7268 (mtt) cc_final: 0.7041 (mtp) REVERT: M 425 MET cc_start: 0.8748 (mmt) cc_final: 0.8457 (mmt) REVERT: P 166 THR cc_start: 0.7760 (t) cc_final: 0.7470 (t) REVERT: P 282 ARG cc_start: 0.7139 (mtp180) cc_final: 0.6884 (mtp85) REVERT: P 325 GLU cc_start: 0.8347 (pp20) cc_final: 0.8014 (pp20) REVERT: P 361 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6639 (mt) REVERT: O 214 ARG cc_start: 0.6222 (tmm160) cc_final: 0.5384 (tpp80) REVERT: R 282 ARG cc_start: 0.7078 (mtp180) cc_final: 0.6711 (mtp85) REVERT: R 303 CYS cc_start: 0.4934 (OUTLIER) cc_final: 0.4644 (p) REVERT: R 363 MET cc_start: 0.3240 (ptt) cc_final: 0.2931 (ptt) REVERT: Q 214 ARG cc_start: 0.6067 (tmm160) cc_final: 0.5284 (tpp80) REVERT: Q 425 MET cc_start: 0.8735 (mmt) cc_final: 0.8420 (mmt) outliers start: 180 outliers final: 25 residues processed: 1456 average time/residue: 0.5018 time to fit residues: 1286.1063 Evaluate side-chains 1026 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 990 time to evaluate : 5.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 299 MET Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 313 MET Chi-restraints excluded: chain N residue 299 MET Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain M residue 11 GLN Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain O residue 11 GLN Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain Q residue 11 GLN Chi-restraints excluded: chain Q residue 313 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 645 optimal weight: 1.9990 chunk 579 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 198 optimal weight: 0.3980 chunk 391 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 599 optimal weight: 0.4980 chunk 232 optimal weight: 0.5980 chunk 364 optimal weight: 0.8980 chunk 446 optimal weight: 0.6980 chunk 694 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 292 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN D 14 ASN D 292 GLN ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN C 18 ASN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN F 14 ASN ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN H 14 ASN H 292 GLN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 14 ASN J 292 GLN ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN I 31 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** L 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN N 14 ASN N 292 GLN ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 ASN M 31 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 228 ASN P 14 ASN P 165 ASN P 292 GLN ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 18 ASN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 ASN R 14 ASN R 292 GLN ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 ASN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 62100 Z= 0.217 Angle : 0.799 18.182 84528 Z= 0.381 Chirality : 0.048 0.211 9342 Planarity : 0.006 0.067 10989 Dihedral : 20.079 179.119 9206 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.22 % Allowed : 13.29 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.09), residues: 7749 helix: -0.29 (0.09), residues: 3159 sheet: -1.20 (0.17), residues: 990 loop : -2.46 (0.10), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 21 HIS 0.006 0.001 HIS R 227 PHE 0.020 0.002 PHE N 378 TYR 0.014 0.001 TYR G 24 ARG 0.003 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1222 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 MET cc_start: 0.7804 (tpp) cc_final: 0.7530 (tpp) REVERT: B 309 ARG cc_start: 0.5164 (mtt-85) cc_final: 0.4857 (mtt-85) REVERT: B 388 MET cc_start: 0.8439 (ttm) cc_final: 0.8101 (ttm) REVERT: A 172 TYR cc_start: 0.7854 (t80) cc_final: 0.6703 (t80) REVERT: A 214 ARG cc_start: 0.6137 (tmm160) cc_final: 0.5353 (tpp80) REVERT: D 167 PHE cc_start: 0.6035 (m-80) cc_final: 0.5308 (m-80) REVERT: D 205 GLU cc_start: 0.9318 (tt0) cc_final: 0.9075 (tt0) REVERT: D 282 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6546 (mtp85) REVERT: D 293 MET cc_start: 0.7727 (tpp) cc_final: 0.7379 (tpp) REVERT: D 406 MET cc_start: 0.8464 (mmp) cc_final: 0.8148 (mmp) REVERT: C 172 TYR cc_start: 0.7846 (t80) cc_final: 0.6888 (t80) REVERT: C 214 ARG cc_start: 0.6163 (tmm160) cc_final: 0.5363 (tpp80) REVERT: C 377 MET cc_start: 0.7343 (mtt) cc_final: 0.7059 (mtp) REVERT: C 423 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8776 (tp30) REVERT: F 14 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8207 (m110) REVERT: F 134 GLN cc_start: 0.8460 (tp40) cc_final: 0.7478 (tp40) REVERT: F 147 MET cc_start: 0.8127 (mmt) cc_final: 0.7592 (tpp) REVERT: F 167 PHE cc_start: 0.6784 (m-80) cc_final: 0.6295 (m-80) REVERT: F 282 ARG cc_start: 0.7328 (mtp180) cc_final: 0.6648 (mtp85) REVERT: F 293 MET cc_start: 0.7678 (tpp) cc_final: 0.7280 (tpp) REVERT: E 432 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: H 267 MET cc_start: 0.8013 (ttt) cc_final: 0.7455 (ttt) REVERT: H 282 ARG cc_start: 0.7052 (mtp180) cc_final: 0.6329 (mtp85) REVERT: H 293 MET cc_start: 0.7856 (tpp) cc_final: 0.7584 (tpp) REVERT: H 388 MET cc_start: 0.8534 (ttm) cc_final: 0.8103 (ttt) REVERT: G 214 ARG cc_start: 0.5830 (tmm160) cc_final: 0.5048 (tpp80) REVERT: G 377 MET cc_start: 0.7299 (mtt) cc_final: 0.6932 (mtp) REVERT: J 257 MET cc_start: 0.9143 (mmp) cc_final: 0.8492 (mmp) REVERT: J 282 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6371 (mtp85) REVERT: J 293 MET cc_start: 0.7736 (tpp) cc_final: 0.7386 (tpp) REVERT: J 363 MET cc_start: 0.3346 (ptt) cc_final: 0.2871 (ptt) REVERT: J 388 MET cc_start: 0.8482 (ttm) cc_final: 0.8230 (ttm) REVERT: I 97 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: I 214 ARG cc_start: 0.6121 (tmm160) cc_final: 0.4992 (tpp80) REVERT: L 293 MET cc_start: 0.8009 (tpp) cc_final: 0.7654 (tpp) REVERT: L 388 MET cc_start: 0.8144 (ttm) cc_final: 0.7917 (ttt) REVERT: K 172 TYR cc_start: 0.7671 (t80) cc_final: 0.6687 (t80) REVERT: K 189 LEU cc_start: 0.9559 (tp) cc_final: 0.9314 (tp) REVERT: K 214 ARG cc_start: 0.6353 (tmm160) cc_final: 0.5495 (tpp80) REVERT: K 233 GLN cc_start: 0.9093 (tp40) cc_final: 0.8824 (mm110) REVERT: K 425 MET cc_start: 0.8630 (mmp) cc_final: 0.8042 (mmt) REVERT: N 282 ARG cc_start: 0.6889 (mtp180) cc_final: 0.6285 (mtp85) REVERT: N 293 MET cc_start: 0.7791 (tpp) cc_final: 0.7573 (tpp) REVERT: N 309 ARG cc_start: 0.5181 (mtt-85) cc_final: 0.4883 (mtt-85) REVERT: M 172 TYR cc_start: 0.7713 (t80) cc_final: 0.6591 (t80) REVERT: M 214 ARG cc_start: 0.6213 (tmm160) cc_final: 0.5368 (tpp80) REVERT: M 313 MET cc_start: 0.7770 (mmm) cc_final: 0.7512 (mmm) REVERT: P 14 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8209 (m-40) REVERT: P 282 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6385 (mtp85) REVERT: P 293 MET cc_start: 0.7663 (tpp) cc_final: 0.7235 (tpp) REVERT: P 309 ARG cc_start: 0.4799 (mtt-85) cc_final: 0.4535 (mtt-85) REVERT: P 321 MET cc_start: 0.7291 (tmm) cc_final: 0.7085 (tmm) REVERT: P 388 MET cc_start: 0.8339 (ttm) cc_final: 0.7986 (ttt) REVERT: O 214 ARG cc_start: 0.6105 (tmm160) cc_final: 0.5251 (tpp80) REVERT: O 233 GLN cc_start: 0.9108 (tp40) cc_final: 0.8895 (tp40) REVERT: O 423 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8755 (tp30) REVERT: R 147 MET cc_start: 0.7985 (mmp) cc_final: 0.7646 (tpp) REVERT: R 257 MET cc_start: 0.9100 (mmp) cc_final: 0.8874 (mmp) REVERT: R 267 MET cc_start: 0.7840 (ttt) cc_final: 0.7392 (ttt) REVERT: R 282 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6486 (mtp85) REVERT: R 293 MET cc_start: 0.7835 (tpp) cc_final: 0.7534 (tpp) REVERT: Q 233 GLN cc_start: 0.9177 (tp40) cc_final: 0.8912 (mm110) outliers start: 204 outliers final: 112 residues processed: 1327 average time/residue: 0.5111 time to fit residues: 1196.0867 Evaluate side-chains 1173 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1057 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 397 TRP Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain L residue 14 ASN Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 207 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 TRP Chi-restraints excluded: chain M residue 11 GLN Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain P residue 14 ASN Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 327 ASP Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 397 TRP Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain R residue 14 ASN Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 397 TRP Chi-restraints excluded: chain Q residue 11 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 228 ASN Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 315 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 386 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 578 optimal weight: 1.9990 chunk 473 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 695 optimal weight: 2.9990 chunk 751 optimal weight: 4.9990 chunk 619 optimal weight: 3.9990 chunk 690 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 558 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 62100 Z= 0.264 Angle : 0.767 19.521 84528 Z= 0.366 Chirality : 0.047 0.198 9342 Planarity : 0.006 0.068 10989 Dihedral : 19.709 177.152 9158 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.70 % Allowed : 18.71 % Favored : 77.59 % 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: -2.00 (0.10), residues: 7749 helix: -0.24 (0.09), residues: 3186 sheet: -1.31 (0.17), residues: 990 loop : -2.36 (0.10), residues: 3573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 21 HIS 0.005 0.001 HIS D 190 PHE 0.020 0.002 PHE N 133 TYR 0.019 0.001 TYR O 262 ARG 0.006 0.001 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1120 time to evaluate : 5.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 267 MET cc_start: 0.7174 (ttt) cc_final: 0.6659 (ttt) REVERT: B 293 MET cc_start: 0.8037 (tpp) cc_final: 0.7727 (tpp) REVERT: B 309 ARG cc_start: 0.5284 (mtt-85) cc_final: 0.4998 (mtt-85) REVERT: A 172 TYR cc_start: 0.8023 (t80) cc_final: 0.6857 (t80) REVERT: A 214 ARG cc_start: 0.6289 (tmm160) cc_final: 0.5505 (tpp80) REVERT: A 313 MET cc_start: 0.8352 (mmm) cc_final: 0.8046 (mmm) REVERT: D 134 GLN cc_start: 0.8199 (tp40) cc_final: 0.7577 (tp40) REVERT: D 147 MET cc_start: 0.7976 (mmp) cc_final: 0.7140 (tpp) REVERT: D 167 PHE cc_start: 0.6557 (m-80) cc_final: 0.6143 (m-80) REVERT: D 282 ARG cc_start: 0.7017 (mtp180) cc_final: 0.6486 (mtp85) REVERT: D 363 MET cc_start: 0.1846 (ptt) cc_final: 0.1214 (pmm) REVERT: D 406 MET cc_start: 0.8509 (mmp) cc_final: 0.8225 (mmp) REVERT: C 97 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: C 172 TYR cc_start: 0.7942 (t80) cc_final: 0.7055 (t80) REVERT: C 214 ARG cc_start: 0.6189 (tmm160) cc_final: 0.5420 (tpp80) REVERT: C 313 MET cc_start: 0.8191 (mmm) cc_final: 0.7335 (mmm) REVERT: C 377 MET cc_start: 0.7454 (mtt) cc_final: 0.7125 (mtp) REVERT: F 14 ASN cc_start: 0.9245 (m-40) cc_final: 0.8813 (m110) REVERT: F 267 MET cc_start: 0.8382 (ttp) cc_final: 0.7698 (ttt) REVERT: F 282 ARG cc_start: 0.7333 (mtp180) cc_final: 0.6459 (mtp85) REVERT: F 363 MET cc_start: 0.1765 (ptt) cc_final: 0.1521 (pmm) REVERT: E 214 ARG cc_start: 0.5941 (tmm160) cc_final: 0.5097 (tpp80) REVERT: E 423 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8776 (tp30) REVERT: H 282 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6213 (mtp85) REVERT: H 289 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5494 (mp) REVERT: H 363 MET cc_start: 0.1821 (ptt) cc_final: 0.1154 (pmm) REVERT: H 388 MET cc_start: 0.8650 (ttm) cc_final: 0.8306 (ttp) REVERT: G 214 ARG cc_start: 0.5941 (tmm160) cc_final: 0.5278 (tpp80) REVERT: G 313 MET cc_start: 0.8268 (mmm) cc_final: 0.7557 (mmm) REVERT: G 377 MET cc_start: 0.7274 (mtt) cc_final: 0.6876 (mtp) REVERT: J 108 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: J 134 GLN cc_start: 0.8331 (tp40) cc_final: 0.8032 (tp40) REVERT: J 257 MET cc_start: 0.9207 (mmp) cc_final: 0.8678 (mmp) REVERT: J 267 MET cc_start: 0.8250 (ttp) cc_final: 0.7792 (ttt) REVERT: J 282 ARG cc_start: 0.7034 (mtp180) cc_final: 0.6347 (mtp85) REVERT: J 293 MET cc_start: 0.7815 (tpp) cc_final: 0.7608 (tpp) REVERT: J 309 ARG cc_start: 0.5326 (mtt-85) cc_final: 0.5016 (mtt-85) REVERT: J 363 MET cc_start: 0.3344 (ptt) cc_final: 0.3030 (ptt) REVERT: J 388 MET cc_start: 0.8527 (ttm) cc_final: 0.8235 (ttm) REVERT: I 313 MET cc_start: 0.8319 (mmm) cc_final: 0.7875 (mmm) REVERT: L 108 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: L 267 MET cc_start: 0.7541 (ttt) cc_final: 0.7182 (ttt) REVERT: L 293 MET cc_start: 0.8057 (tpp) cc_final: 0.7703 (tpp) REVERT: L 363 MET cc_start: 0.2378 (ptt) cc_final: 0.2022 (pmm) REVERT: K 214 ARG cc_start: 0.6535 (tmm160) cc_final: 0.5734 (tpp80) REVERT: N 134 GLN cc_start: 0.8576 (tp40) cc_final: 0.8375 (tp40) REVERT: N 147 MET cc_start: 0.7930 (mmp) cc_final: 0.7340 (tpp) REVERT: N 282 ARG cc_start: 0.6921 (mtp180) cc_final: 0.6362 (mtp85) REVERT: N 309 ARG cc_start: 0.5315 (mtt-85) cc_final: 0.5080 (mtt-85) REVERT: M 214 ARG cc_start: 0.6505 (tmm160) cc_final: 0.5617 (tpp80) REVERT: M 249 ASN cc_start: 0.8152 (m110) cc_final: 0.7925 (m-40) REVERT: M 313 MET cc_start: 0.8061 (mmm) cc_final: 0.7422 (mmm) REVERT: M 377 MET cc_start: 0.6870 (mtp) cc_final: 0.6667 (mtp) REVERT: P 147 MET cc_start: 0.7993 (mmp) cc_final: 0.7322 (tpp) REVERT: P 282 ARG cc_start: 0.7057 (mtp180) cc_final: 0.6239 (mtp85) REVERT: P 289 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5549 (mp) REVERT: P 293 MET cc_start: 0.7853 (tpp) cc_final: 0.7249 (tpp) REVERT: P 309 ARG cc_start: 0.4869 (mtt-85) cc_final: 0.4614 (mtt-85) REVERT: P 363 MET cc_start: 0.1998 (ptt) cc_final: 0.1708 (pmm) REVERT: P 388 MET cc_start: 0.8483 (ttm) cc_final: 0.7981 (ttm) REVERT: O 214 ARG cc_start: 0.6201 (tmm160) cc_final: 0.5266 (tpp80) REVERT: O 423 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8771 (tp30) REVERT: R 147 MET cc_start: 0.7876 (mmp) cc_final: 0.7171 (mmp) REVERT: R 267 MET cc_start: 0.7462 (ttt) cc_final: 0.7055 (ttt) REVERT: R 282 ARG cc_start: 0.6837 (mtp180) cc_final: 0.6118 (mtp85) REVERT: R 289 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5392 (mp) REVERT: R 363 MET cc_start: 0.1531 (ptt) cc_final: 0.1039 (pmm) outliers start: 235 outliers final: 147 residues processed: 1257 average time/residue: 0.5534 time to fit residues: 1233.0213 Evaluate side-chains 1188 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1035 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 300 MET Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 258 VAL Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 108 GLU Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 165 ASN Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 207 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 11 GLN Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 210 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 228 ASN Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 315 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 687 optimal weight: 1.9990 chunk 523 optimal weight: 4.9990 chunk 361 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 332 optimal weight: 0.0770 chunk 467 optimal weight: 7.9990 chunk 698 optimal weight: 0.9980 chunk 739 optimal weight: 1.9990 chunk 364 optimal weight: 3.9990 chunk 661 optimal weight: 2.9990 chunk 199 optimal weight: 0.0670 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 228 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 62100 Z= 0.200 Angle : 0.730 18.542 84528 Z= 0.343 Chirality : 0.045 0.201 9342 Planarity : 0.005 0.062 10989 Dihedral : 19.326 179.982 9143 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.69 % Allowed : 21.37 % Favored : 74.94 % 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: -1.76 (0.10), residues: 7749 helix: -0.08 (0.09), residues: 3168 sheet: -1.19 (0.18), residues: 891 loop : -2.16 (0.10), residues: 3690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 346 HIS 0.005 0.001 HIS L 190 PHE 0.020 0.001 PHE H 378 TYR 0.018 0.001 TYR O 262 ARG 0.005 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1139 time to evaluate : 5.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9216 (m-40) cc_final: 0.8697 (m-40) REVERT: B 267 MET cc_start: 0.7148 (ttt) cc_final: 0.6556 (ttt) REVERT: B 293 MET cc_start: 0.8118 (tpp) cc_final: 0.7700 (tpp) REVERT: B 309 ARG cc_start: 0.5195 (mtt-85) cc_final: 0.4912 (mtt-85) REVERT: A 214 ARG cc_start: 0.6386 (tmm160) cc_final: 0.5689 (tpp80) REVERT: A 313 MET cc_start: 0.8426 (mmm) cc_final: 0.8039 (mmm) REVERT: D 14 ASN cc_start: 0.9167 (m-40) cc_final: 0.8781 (m-40) REVERT: D 108 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: D 134 GLN cc_start: 0.8287 (tp40) cc_final: 0.7833 (tp40) REVERT: D 137 HIS cc_start: 0.8301 (p90) cc_final: 0.7680 (p90) REVERT: D 147 MET cc_start: 0.7913 (mmp) cc_final: 0.7307 (tpp) REVERT: D 164 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6920 (mmp) REVERT: D 167 PHE cc_start: 0.6563 (m-80) cc_final: 0.6345 (m-80) REVERT: D 282 ARG cc_start: 0.7026 (mtp180) cc_final: 0.6469 (mtp85) REVERT: D 285 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7203 (t) REVERT: D 299 MET cc_start: 0.7863 (ptp) cc_final: 0.6865 (mpp) REVERT: D 363 MET cc_start: 0.1435 (ptt) cc_final: 0.0972 (pmm) REVERT: D 406 MET cc_start: 0.8391 (mmp) cc_final: 0.8133 (mmp) REVERT: C 97 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: C 172 TYR cc_start: 0.7871 (t80) cc_final: 0.6915 (t80) REVERT: C 214 ARG cc_start: 0.6213 (tmm160) cc_final: 0.5473 (tpp80) REVERT: C 313 MET cc_start: 0.8393 (mmm) cc_final: 0.7666 (mmm) REVERT: C 347 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7593 (t) REVERT: C 423 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8782 (tp30) REVERT: F 108 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6463 (pm20) REVERT: F 134 GLN cc_start: 0.8671 (tp40) cc_final: 0.8152 (tp40) REVERT: F 267 MET cc_start: 0.8345 (ttp) cc_final: 0.7745 (ttt) REVERT: F 282 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6444 (mtp85) REVERT: F 293 MET cc_start: 0.7855 (tpp) cc_final: 0.7585 (tpp) REVERT: F 299 MET cc_start: 0.7737 (ptp) cc_final: 0.7031 (mpp) REVERT: E 214 ARG cc_start: 0.5964 (tmm160) cc_final: 0.5102 (tpp80) REVERT: E 225 THR cc_start: 0.3797 (OUTLIER) cc_final: 0.3584 (m) REVERT: E 423 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8789 (tp30) REVERT: H 108 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: H 267 MET cc_start: 0.7945 (ttt) cc_final: 0.7444 (ttt) REVERT: H 282 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6059 (mtp85) REVERT: H 293 MET cc_start: 0.7774 (tpp) cc_final: 0.7337 (tpp) REVERT: H 363 MET cc_start: 0.1381 (ptt) cc_final: 0.0984 (pmm) REVERT: H 388 MET cc_start: 0.8664 (ttm) cc_final: 0.8285 (ttm) REVERT: G 202 PHE cc_start: 0.7420 (m-80) cc_final: 0.7040 (m-80) REVERT: G 214 ARG cc_start: 0.6017 (tmm160) cc_final: 0.5362 (tpp80) REVERT: G 225 THR cc_start: 0.3612 (OUTLIER) cc_final: 0.3355 (m) REVERT: G 313 MET cc_start: 0.8303 (mmm) cc_final: 0.7618 (mmm) REVERT: G 377 MET cc_start: 0.7228 (mtt) cc_final: 0.6837 (mtp) REVERT: J 134 GLN cc_start: 0.8267 (tp40) cc_final: 0.8027 (tp40) REVERT: J 257 MET cc_start: 0.9159 (mmp) cc_final: 0.8646 (mmp) REVERT: J 282 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6340 (mtp85) REVERT: J 309 ARG cc_start: 0.5510 (mtt-85) cc_final: 0.5187 (mtt-85) REVERT: J 363 MET cc_start: 0.3219 (ptt) cc_final: 0.2999 (ptt) REVERT: I 225 THR cc_start: 0.3351 (OUTLIER) cc_final: 0.3070 (m) REVERT: I 313 MET cc_start: 0.8457 (mmm) cc_final: 0.7823 (mmm) REVERT: I 347 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7237 (t) REVERT: L 257 MET cc_start: 0.8714 (mmm) cc_final: 0.8456 (mmm) REVERT: L 267 MET cc_start: 0.7517 (ttt) cc_final: 0.7146 (ttt) REVERT: L 293 MET cc_start: 0.8039 (tpp) cc_final: 0.7697 (tpp) REVERT: L 363 MET cc_start: 0.2063 (ptt) cc_final: 0.1833 (pmm) REVERT: K 172 TYR cc_start: 0.7709 (t80) cc_final: 0.6808 (t80) REVERT: K 214 ARG cc_start: 0.6575 (tmm160) cc_final: 0.5804 (tpp80) REVERT: K 313 MET cc_start: 0.8399 (mmm) cc_final: 0.7975 (mmm) REVERT: K 347 CYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7261 (t) REVERT: K 377 MET cc_start: 0.6739 (mtp) cc_final: 0.6308 (mtp) REVERT: N 134 GLN cc_start: 0.8585 (tp40) cc_final: 0.8359 (tp40) REVERT: N 147 MET cc_start: 0.7911 (mmp) cc_final: 0.7459 (tpp) REVERT: N 257 MET cc_start: 0.9101 (mmp) cc_final: 0.8821 (mmp) REVERT: N 282 ARG cc_start: 0.6926 (mtp180) cc_final: 0.6321 (mtp85) REVERT: N 293 MET cc_start: 0.7740 (tpp) cc_final: 0.7511 (tpp) REVERT: N 309 ARG cc_start: 0.5326 (mtt-85) cc_final: 0.5079 (mtt-85) REVERT: M 214 ARG cc_start: 0.6564 (tmm160) cc_final: 0.5700 (tpp80) REVERT: M 225 THR cc_start: 0.3206 (OUTLIER) cc_final: 0.3005 (m) REVERT: M 249 ASN cc_start: 0.8087 (m110) cc_final: 0.7840 (m-40) REVERT: M 313 MET cc_start: 0.8093 (mmm) cc_final: 0.7511 (mmm) REVERT: M 377 MET cc_start: 0.6744 (mtp) cc_final: 0.6489 (mtp) REVERT: P 134 GLN cc_start: 0.8354 (tp40) cc_final: 0.7846 (tp-100) REVERT: P 147 MET cc_start: 0.7751 (mmp) cc_final: 0.7463 (tpp) REVERT: P 267 MET cc_start: 0.8469 (ttp) cc_final: 0.8121 (ttt) REVERT: P 282 ARG cc_start: 0.7089 (mtp180) cc_final: 0.6231 (mtp85) REVERT: P 289 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5481 (mp) REVERT: P 293 MET cc_start: 0.7950 (tpp) cc_final: 0.7430 (tpp) REVERT: P 388 MET cc_start: 0.8508 (ttm) cc_final: 0.7999 (ttm) REVERT: O 214 ARG cc_start: 0.6166 (tmm160) cc_final: 0.5249 (tpp80) REVERT: O 423 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8782 (tp30) REVERT: R 147 MET cc_start: 0.7820 (mmp) cc_final: 0.7331 (mmp) REVERT: R 257 MET cc_start: 0.9162 (mmp) cc_final: 0.8799 (mmp) REVERT: R 267 MET cc_start: 0.7390 (ttt) cc_final: 0.6867 (ttt) REVERT: R 282 ARG cc_start: 0.6869 (mtp180) cc_final: 0.6102 (mtp85) REVERT: R 289 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.5371 (mp) REVERT: R 293 MET cc_start: 0.7999 (tpp) cc_final: 0.7581 (tpp) REVERT: R 363 MET cc_start: 0.1417 (ptt) cc_final: 0.1005 (pmm) REVERT: Q 259 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (mm) REVERT: Q 413 MET cc_start: 0.8553 (ppp) cc_final: 0.8189 (tmm) outliers start: 234 outliers final: 150 residues processed: 1276 average time/residue: 0.5065 time to fit residues: 1135.9466 Evaluate side-chains 1245 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1079 time to evaluate : 5.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 108 GLU Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 274 THR Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 207 LEU Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 300 MET Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 225 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 274 THR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 145 THR Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 210 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 315 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 615 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 550 optimal weight: 2.9990 chunk 305 optimal weight: 0.0170 chunk 631 optimal weight: 4.9990 chunk 511 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 663 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 15 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 15 GLN K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 62100 Z= 0.353 Angle : 0.802 19.455 84528 Z= 0.387 Chirality : 0.048 0.232 9342 Planarity : 0.006 0.064 10989 Dihedral : 19.337 179.257 9120 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 4.79 % Allowed : 23.37 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.09), residues: 7749 helix: -0.32 (0.09), residues: 3195 sheet: -1.55 (0.17), residues: 990 loop : -2.23 (0.10), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 397 HIS 0.014 0.001 HIS M 107 PHE 0.023 0.002 PHE H 133 TYR 0.016 0.002 TYR Q 24 ARG 0.005 0.001 ARG L 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1091 time to evaluate : 5.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 14 ASN cc_start: 0.9386 (m-40) cc_final: 0.8820 (m-40) REVERT: B 267 MET cc_start: 0.7822 (ttt) cc_final: 0.7372 (ttt) REVERT: B 293 MET cc_start: 0.8003 (tpp) cc_final: 0.7764 (tpp) REVERT: B 299 MET cc_start: 0.8125 (ptp) cc_final: 0.7118 (mpp) REVERT: B 309 ARG cc_start: 0.5269 (mtt-85) cc_final: 0.5014 (mtt-85) REVERT: A 313 MET cc_start: 0.8332 (mmm) cc_final: 0.7903 (mmm) REVERT: A 347 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7380 (t) REVERT: D 14 ASN cc_start: 0.9311 (m-40) cc_final: 0.8860 (m-40) REVERT: D 108 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: D 147 MET cc_start: 0.8079 (mmp) cc_final: 0.7543 (tpp) REVERT: D 213 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7771 (mtp85) REVERT: D 282 ARG cc_start: 0.6933 (mtp180) cc_final: 0.6069 (mtp85) REVERT: D 285 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7298 (t) REVERT: D 286 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.6534 (m) REVERT: D 363 MET cc_start: 0.2577 (ptt) cc_final: 0.1691 (pmm) REVERT: D 406 MET cc_start: 0.8576 (mmp) cc_final: 0.8346 (mmp) REVERT: C 279 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 313 MET cc_start: 0.8524 (mmm) cc_final: 0.7571 (mmm) REVERT: C 347 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7696 (t) REVERT: F 267 MET cc_start: 0.8466 (ttp) cc_final: 0.8060 (ttt) REVERT: F 282 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6355 (mtp85) REVERT: F 293 MET cc_start: 0.7982 (tpp) cc_final: 0.7690 (tpp) REVERT: E 214 ARG cc_start: 0.6002 (tmm160) cc_final: 0.4987 (tpp80) REVERT: H 267 MET cc_start: 0.8199 (ttt) cc_final: 0.7673 (ttt) REVERT: H 282 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6147 (mtp85) REVERT: H 286 VAL cc_start: 0.7240 (OUTLIER) cc_final: 0.6829 (m) REVERT: H 293 MET cc_start: 0.7847 (tpp) cc_final: 0.7615 (tpp) REVERT: H 299 MET cc_start: 0.8214 (ptp) cc_final: 0.6930 (mpp) REVERT: H 363 MET cc_start: 0.1755 (ptt) cc_final: 0.1003 (pmm) REVERT: H 388 MET cc_start: 0.8527 (ttm) cc_final: 0.8065 (ttm) REVERT: G 202 PHE cc_start: 0.7489 (m-80) cc_final: 0.6939 (m-80) REVERT: G 225 THR cc_start: 0.3888 (OUTLIER) cc_final: 0.3624 (m) REVERT: G 296 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: G 313 MET cc_start: 0.8512 (mmm) cc_final: 0.7827 (mmm) REVERT: G 347 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7458 (t) REVERT: G 377 MET cc_start: 0.7271 (mtt) cc_final: 0.6900 (mtp) REVERT: J 108 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: J 134 GLN cc_start: 0.8350 (tp40) cc_final: 0.8106 (tp40) REVERT: J 257 MET cc_start: 0.9301 (mmp) cc_final: 0.8809 (mmp) REVERT: J 282 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6430 (mtp85) REVERT: J 309 ARG cc_start: 0.5523 (mtt-85) cc_final: 0.5204 (mtt-85) REVERT: J 363 MET cc_start: 0.3688 (ptt) cc_final: 0.3419 (ptt) REVERT: J 388 MET cc_start: 0.8301 (ttm) cc_final: 0.8090 (ttm) REVERT: I 36 MET cc_start: 0.5877 (mpp) cc_final: 0.5552 (mmt) REVERT: I 225 THR cc_start: 0.3716 (OUTLIER) cc_final: 0.3451 (m) REVERT: I 313 MET cc_start: 0.8533 (mmm) cc_final: 0.7130 (tpp) REVERT: I 347 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7301 (t) REVERT: L 253 LEU cc_start: 0.9556 (mt) cc_final: 0.9319 (mt) REVERT: L 293 MET cc_start: 0.8144 (tpp) cc_final: 0.7805 (tpp) REVERT: L 363 MET cc_start: 0.2755 (ptt) cc_final: 0.2123 (pmm) REVERT: K 214 ARG cc_start: 0.6518 (tmm160) cc_final: 0.5511 (tpp80) REVERT: K 279 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7527 (mm-30) REVERT: K 313 MET cc_start: 0.8371 (mmm) cc_final: 0.7003 (tpp) REVERT: N 147 MET cc_start: 0.7982 (mmp) cc_final: 0.7602 (tpp) REVERT: N 282 ARG cc_start: 0.7089 (mtp180) cc_final: 0.6407 (mtp85) REVERT: N 309 ARG cc_start: 0.5500 (mtt-85) cc_final: 0.5259 (mtt-85) REVERT: M 24 TYR cc_start: 0.4841 (OUTLIER) cc_final: 0.3311 (t80) REVERT: M 214 ARG cc_start: 0.6584 (tmm160) cc_final: 0.5750 (tpp80) REVERT: M 249 ASN cc_start: 0.8037 (m110) cc_final: 0.7765 (m-40) REVERT: M 313 MET cc_start: 0.8332 (mmm) cc_final: 0.7523 (mmm) REVERT: M 347 CYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7477 (t) REVERT: M 377 MET cc_start: 0.6828 (mtp) cc_final: 0.6582 (mtp) REVERT: P 14 ASN cc_start: 0.9364 (m-40) cc_final: 0.8788 (m-40) REVERT: P 147 MET cc_start: 0.8117 (mmp) cc_final: 0.7831 (tpp) REVERT: P 267 MET cc_start: 0.8528 (ttp) cc_final: 0.8268 (ttt) REVERT: P 282 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6196 (mtp85) REVERT: P 289 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5658 (mp) REVERT: P 293 MET cc_start: 0.8006 (tpp) cc_final: 0.7515 (tpp) REVERT: P 309 ARG cc_start: 0.5108 (mtt-85) cc_final: 0.4850 (mtt-85) REVERT: O 302 MET cc_start: 0.7980 (mmt) cc_final: 0.7763 (mmp) REVERT: O 313 MET cc_start: 0.8592 (mmm) cc_final: 0.7288 (tpp) REVERT: O 347 CYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7362 (t) REVERT: O 413 MET cc_start: 0.8443 (ttp) cc_final: 0.8200 (tmm) REVERT: O 423 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8804 (tp30) REVERT: R 282 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6042 (mtp85) REVERT: R 303 CYS cc_start: 0.4559 (OUTLIER) cc_final: 0.4297 (p) REVERT: Q 24 TYR cc_start: 0.4567 (OUTLIER) cc_final: 0.3300 (t80) REVERT: Q 259 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8621 (mm) REVERT: Q 279 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7238 (mm-30) outliers start: 304 outliers final: 239 residues processed: 1276 average time/residue: 0.5155 time to fit residues: 1157.9941 Evaluate side-chains 1303 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1045 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain G residue 4 CYS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 108 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 11 GLN Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 207 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 233 MET Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 24 TYR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 296 PHE Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 274 THR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 363 MET Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 4 CYS Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 296 PHE Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 210 ILE Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 4 CYS Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 24 TYR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 248 optimal weight: 0.3980 chunk 665 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 434 optimal weight: 0.9980 chunk 182 optimal weight: 0.1980 chunk 740 optimal weight: 0.9980 chunk 614 optimal weight: 1.9990 chunk 342 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 244 optimal weight: 0.4980 chunk 388 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 228 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 165 ASN ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 101 ASN ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 GLN ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 62100 Z= 0.183 Angle : 0.729 18.030 84528 Z= 0.341 Chirality : 0.045 0.250 9342 Planarity : 0.005 0.064 10989 Dihedral : 18.837 179.196 9120 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.37 % Allowed : 25.99 % Favored : 70.64 % 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: -1.70 (0.10), residues: 7749 helix: -0.07 (0.10), residues: 3150 sheet: -1.24 (0.18), residues: 945 loop : -2.06 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 21 HIS 0.010 0.001 HIS M 107 PHE 0.027 0.001 PHE J 133 TYR 0.021 0.001 TYR K 432 ARG 0.004 0.000 ARG G 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1138 time to evaluate : 5.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 14 ASN cc_start: 0.9347 (m-40) cc_final: 0.8806 (m-40) REVERT: B 267 MET cc_start: 0.7271 (ttt) cc_final: 0.6819 (ttt) REVERT: B 293 MET cc_start: 0.8034 (tpp) cc_final: 0.7825 (tpp) REVERT: A 36 MET cc_start: 0.5381 (mpp) cc_final: 0.5064 (mmt) REVERT: A 313 MET cc_start: 0.8447 (mmm) cc_final: 0.8219 (mmm) REVERT: A 347 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7383 (t) REVERT: D 108 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: D 134 GLN cc_start: 0.8392 (tp40) cc_final: 0.8190 (tp40) REVERT: D 137 HIS cc_start: 0.8249 (p90) cc_final: 0.7826 (p-80) REVERT: D 147 MET cc_start: 0.8016 (mmp) cc_final: 0.7703 (tpp) REVERT: D 282 ARG cc_start: 0.6924 (mtp180) cc_final: 0.6117 (mtp85) REVERT: D 285 THR cc_start: 0.7336 (OUTLIER) cc_final: 0.7126 (t) REVERT: D 286 VAL cc_start: 0.6778 (OUTLIER) cc_final: 0.6480 (m) REVERT: D 363 MET cc_start: 0.1955 (ptt) cc_final: 0.1507 (pmm) REVERT: D 370 ASN cc_start: 0.8488 (t0) cc_final: 0.7209 (m-40) REVERT: D 406 MET cc_start: 0.8366 (mmp) cc_final: 0.8142 (mmp) REVERT: C 36 MET cc_start: 0.6072 (mpp) cc_final: 0.5686 (mmt) REVERT: C 172 TYR cc_start: 0.7781 (t80) cc_final: 0.6928 (t80) REVERT: C 279 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 313 MET cc_start: 0.8534 (mmm) cc_final: 0.7671 (tpp) REVERT: C 315 CYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7771 (p) REVERT: C 347 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7658 (t) REVERT: C 377 MET cc_start: 0.7301 (mtt) cc_final: 0.6984 (mtp) REVERT: C 423 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8857 (tp30) REVERT: F 99 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6910 (p0) REVERT: F 147 MET cc_start: 0.8287 (mmt) cc_final: 0.7879 (tpp) REVERT: F 257 MET cc_start: 0.9008 (mmp) cc_final: 0.8711 (mmp) REVERT: F 267 MET cc_start: 0.8378 (ttp) cc_final: 0.7586 (ttm) REVERT: F 282 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6554 (mtp85) REVERT: F 293 MET cc_start: 0.7920 (tpp) cc_final: 0.7633 (tpp) REVERT: E 36 MET cc_start: 0.5451 (mpp) cc_final: 0.5215 (mmt) REVERT: E 347 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7675 (t) REVERT: H 14 ASN cc_start: 0.9258 (m-40) cc_final: 0.8726 (m-40) REVERT: H 267 MET cc_start: 0.8008 (ttt) cc_final: 0.7551 (ttt) REVERT: H 282 ARG cc_start: 0.7139 (mtp180) cc_final: 0.6159 (mtp85) REVERT: H 293 MET cc_start: 0.7908 (tpp) cc_final: 0.7677 (tpp) REVERT: H 388 MET cc_start: 0.8526 (ttm) cc_final: 0.8127 (ttm) REVERT: G 202 PHE cc_start: 0.7382 (m-80) cc_final: 0.7035 (m-80) REVERT: G 225 THR cc_start: 0.3714 (OUTLIER) cc_final: 0.3482 (m) REVERT: G 296 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5703 (m-80) REVERT: G 313 MET cc_start: 0.8409 (mmm) cc_final: 0.7763 (mmm) REVERT: G 347 CYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7400 (t) REVERT: G 377 MET cc_start: 0.7316 (mtt) cc_final: 0.6911 (mtp) REVERT: J 134 GLN cc_start: 0.8304 (tp40) cc_final: 0.7959 (tp40) REVERT: J 147 MET cc_start: 0.8244 (mmt) cc_final: 0.7667 (tpp) REVERT: J 257 MET cc_start: 0.9189 (mmp) cc_final: 0.8795 (mmp) REVERT: J 267 MET cc_start: 0.8244 (ttp) cc_final: 0.7570 (ttm) REVERT: J 282 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6483 (mtp85) REVERT: J 293 MET cc_start: 0.7818 (tpp) cc_final: 0.7522 (tpp) REVERT: J 300 MET cc_start: 0.7764 (mpp) cc_final: 0.6814 (pmm) REVERT: J 309 ARG cc_start: 0.5604 (mtt-85) cc_final: 0.5273 (mtt-85) REVERT: J 367 PHE cc_start: 0.7839 (t80) cc_final: 0.6645 (t80) REVERT: J 388 MET cc_start: 0.8389 (ttm) cc_final: 0.8168 (ttm) REVERT: I 172 TYR cc_start: 0.7789 (t80) cc_final: 0.7186 (t80) REVERT: I 225 THR cc_start: 0.3559 (OUTLIER) cc_final: 0.3331 (m) REVERT: I 313 MET cc_start: 0.8533 (mmm) cc_final: 0.7850 (mmm) REVERT: I 347 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7262 (t) REVERT: L 14 ASN cc_start: 0.9299 (m-40) cc_final: 0.8886 (m-40) REVERT: L 253 LEU cc_start: 0.9547 (mt) cc_final: 0.9342 (mt) REVERT: L 267 MET cc_start: 0.7480 (ttt) cc_final: 0.7127 (ttt) REVERT: L 293 MET cc_start: 0.8117 (tpp) cc_final: 0.7833 (tpp) REVERT: L 363 MET cc_start: 0.2390 (ptt) cc_final: 0.2097 (pmm) REVERT: K 172 TYR cc_start: 0.7655 (t80) cc_final: 0.6743 (t80) REVERT: K 214 ARG cc_start: 0.6467 (tmm160) cc_final: 0.5677 (tpp80) REVERT: K 279 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7648 (mm-30) REVERT: K 313 MET cc_start: 0.8504 (mmm) cc_final: 0.7654 (tpp) REVERT: K 347 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7629 (t) REVERT: K 377 MET cc_start: 0.6756 (mtp) cc_final: 0.6285 (mtp) REVERT: N 147 MET cc_start: 0.7938 (mmp) cc_final: 0.7690 (tpp) REVERT: N 267 MET cc_start: 0.7142 (ttt) cc_final: 0.6869 (ttt) REVERT: N 282 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6358 (mtp85) REVERT: N 309 ARG cc_start: 0.5380 (mtt-85) cc_final: 0.5133 (mtt-85) REVERT: M 24 TYR cc_start: 0.4773 (OUTLIER) cc_final: 0.3206 (t80) REVERT: M 172 TYR cc_start: 0.7633 (t80) cc_final: 0.7406 (t80) REVERT: M 214 ARG cc_start: 0.6434 (tmm160) cc_final: 0.5675 (tpp80) REVERT: M 234 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7853 (mt) REVERT: M 249 ASN cc_start: 0.8126 (m110) cc_final: 0.7792 (m-40) REVERT: M 312 TYR cc_start: 0.8415 (m-10) cc_final: 0.8192 (m-10) REVERT: M 313 MET cc_start: 0.8159 (mmm) cc_final: 0.7525 (mmm) REVERT: M 347 CYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7429 (t) REVERT: P 14 ASN cc_start: 0.9290 (m-40) cc_final: 0.8842 (m-40) REVERT: P 134 GLN cc_start: 0.8512 (tp40) cc_final: 0.8132 (tp-100) REVERT: P 267 MET cc_start: 0.8482 (ttp) cc_final: 0.8176 (ttt) REVERT: P 282 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6241 (mtp85) REVERT: P 289 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5592 (mp) REVERT: P 293 MET cc_start: 0.8086 (tpp) cc_final: 0.7620 (tpp) REVERT: P 309 ARG cc_start: 0.5117 (mtt-85) cc_final: 0.4900 (mtt-85) REVERT: P 388 MET cc_start: 0.8472 (ttm) cc_final: 0.8012 (ttm) REVERT: P 403 MET cc_start: 0.8847 (mmm) cc_final: 0.8622 (tpt) REVERT: O 214 ARG cc_start: 0.5897 (tmm-80) cc_final: 0.5380 (tpp80) REVERT: O 313 MET cc_start: 0.8532 (mmm) cc_final: 0.8100 (tpp) REVERT: O 347 CYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7600 (t) REVERT: O 413 MET cc_start: 0.8344 (ttp) cc_final: 0.8142 (tmm) REVERT: R 14 ASN cc_start: 0.9311 (m-40) cc_final: 0.8846 (m-40) REVERT: R 267 MET cc_start: 0.7389 (ttt) cc_final: 0.6880 (ttt) REVERT: R 282 ARG cc_start: 0.6866 (mtp180) cc_final: 0.6085 (mtp85) REVERT: R 293 MET cc_start: 0.8014 (tpp) cc_final: 0.7774 (tpp) REVERT: Q 24 TYR cc_start: 0.4818 (OUTLIER) cc_final: 0.3386 (t80) REVERT: Q 259 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8645 (mm) REVERT: Q 279 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7301 (mm-30) REVERT: Q 347 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7452 (t) REVERT: Q 413 MET cc_start: 0.8326 (ppp) cc_final: 0.8020 (tmm) outliers start: 214 outliers final: 140 residues processed: 1286 average time/residue: 0.5079 time to fit residues: 1148.7956 Evaluate side-chains 1248 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1086 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 225 LEU Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 207 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 24 TYR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 24 TYR Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 347 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 713 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 421 optimal weight: 0.4980 chunk 540 optimal weight: 8.9990 chunk 418 optimal weight: 0.6980 chunk 623 optimal weight: 0.9980 chunk 413 optimal weight: 0.7980 chunk 737 optimal weight: 0.5980 chunk 461 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 ASN ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62100 Z= 0.193 Angle : 0.721 18.096 84528 Z= 0.337 Chirality : 0.044 0.201 9342 Planarity : 0.005 0.059 10989 Dihedral : 18.743 178.752 9120 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.56 % Allowed : 26.56 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.10), residues: 7749 helix: -0.03 (0.10), residues: 3159 sheet: -1.20 (0.18), residues: 936 loop : -2.00 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 21 HIS 0.008 0.001 HIS M 107 PHE 0.024 0.001 PHE F 133 TYR 0.019 0.001 TYR A 103 ARG 0.004 0.000 ARG N 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1124 time to evaluate : 5.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9357 (m-40) cc_final: 0.8817 (m-40) REVERT: B 267 MET cc_start: 0.7237 (ttt) cc_final: 0.6597 (ttt) REVERT: B 293 MET cc_start: 0.8028 (tpp) cc_final: 0.7705 (tpp) REVERT: A 36 MET cc_start: 0.5366 (mpp) cc_final: 0.5060 (mmt) REVERT: A 313 MET cc_start: 0.8312 (mmm) cc_final: 0.7913 (mmm) REVERT: A 347 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7333 (t) REVERT: D 14 ASN cc_start: 0.9323 (m-40) cc_final: 0.8867 (m-40) REVERT: D 108 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: D 134 GLN cc_start: 0.8414 (tp40) cc_final: 0.8106 (tp40) REVERT: D 147 MET cc_start: 0.7991 (mmp) cc_final: 0.7743 (tpp) REVERT: D 282 ARG cc_start: 0.6916 (mtp180) cc_final: 0.6024 (mtp85) REVERT: D 285 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7126 (t) REVERT: D 363 MET cc_start: 0.1898 (ptt) cc_final: 0.1441 (pmm) REVERT: D 370 ASN cc_start: 0.8391 (t0) cc_final: 0.7132 (m-40) REVERT: D 406 MET cc_start: 0.8369 (mmp) cc_final: 0.8162 (mmp) REVERT: C 172 TYR cc_start: 0.7795 (t80) cc_final: 0.6971 (t80) REVERT: C 313 MET cc_start: 0.8600 (mmm) cc_final: 0.7773 (tpp) REVERT: C 315 CYS cc_start: 0.8145 (m) cc_final: 0.7803 (p) REVERT: C 347 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7630 (t) REVERT: C 377 MET cc_start: 0.7294 (mtt) cc_final: 0.6980 (mtp) REVERT: C 423 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8848 (tp30) REVERT: F 14 ASN cc_start: 0.9283 (m-40) cc_final: 0.8753 (m-40) REVERT: F 147 MET cc_start: 0.8328 (mmt) cc_final: 0.7966 (tpp) REVERT: F 257 MET cc_start: 0.9028 (mmp) cc_final: 0.8736 (mmp) REVERT: F 267 MET cc_start: 0.8435 (ttp) cc_final: 0.7741 (ttm) REVERT: F 282 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6664 (mtp85) REVERT: F 293 MET cc_start: 0.7908 (tpp) cc_final: 0.7537 (tpp) REVERT: E 36 MET cc_start: 0.5490 (mpp) cc_final: 0.5262 (mmt) REVERT: E 413 MET cc_start: 0.7821 (tmm) cc_final: 0.7595 (tmm) REVERT: E 423 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8854 (tp30) REVERT: H 14 ASN cc_start: 0.9288 (m-40) cc_final: 0.8846 (m-40) REVERT: H 267 MET cc_start: 0.8030 (ttt) cc_final: 0.7548 (ttt) REVERT: H 282 ARG cc_start: 0.7195 (mtp180) cc_final: 0.6210 (mtp85) REVERT: H 293 MET cc_start: 0.7971 (tpp) cc_final: 0.7693 (tpp) REVERT: H 299 MET cc_start: 0.8007 (ptp) cc_final: 0.7000 (mpp) REVERT: H 388 MET cc_start: 0.8539 (ttm) cc_final: 0.8155 (ttm) REVERT: G 202 PHE cc_start: 0.7358 (m-80) cc_final: 0.6994 (m-80) REVERT: G 214 ARG cc_start: 0.5711 (tmm-80) cc_final: 0.5334 (tpp80) REVERT: G 225 THR cc_start: 0.3903 (OUTLIER) cc_final: 0.3661 (m) REVERT: G 279 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7415 (mm-30) REVERT: G 296 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: G 313 MET cc_start: 0.8457 (mmm) cc_final: 0.7898 (mmm) REVERT: G 347 CYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7382 (t) REVERT: G 377 MET cc_start: 0.7327 (mtt) cc_final: 0.6907 (mtp) REVERT: J 99 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6747 (p0) REVERT: J 134 GLN cc_start: 0.8307 (tp40) cc_final: 0.7985 (tp40) REVERT: J 147 MET cc_start: 0.8194 (mmt) cc_final: 0.7654 (tpp) REVERT: J 282 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6505 (mtp85) REVERT: J 293 MET cc_start: 0.7863 (tpp) cc_final: 0.7587 (tpp) REVERT: J 309 ARG cc_start: 0.5537 (mtt-85) cc_final: 0.5211 (mtt-85) REVERT: J 367 PHE cc_start: 0.7978 (t80) cc_final: 0.6746 (t80) REVERT: J 370 ASN cc_start: 0.8457 (t0) cc_final: 0.7569 (t0) REVERT: I 172 TYR cc_start: 0.7835 (t80) cc_final: 0.7167 (t80) REVERT: I 225 THR cc_start: 0.3387 (OUTLIER) cc_final: 0.3186 (m) REVERT: I 313 MET cc_start: 0.8578 (mmm) cc_final: 0.7946 (mmm) REVERT: I 347 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7293 (t) REVERT: I 423 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8813 (tp30) REVERT: L 14 ASN cc_start: 0.9328 (m-40) cc_final: 0.8896 (m-40) REVERT: L 147 MET cc_start: 0.8225 (mmt) cc_final: 0.7658 (tpp) REVERT: L 253 LEU cc_start: 0.9570 (mt) cc_final: 0.9363 (mt) REVERT: L 293 MET cc_start: 0.8092 (tpp) cc_final: 0.7774 (tpp) REVERT: L 363 MET cc_start: 0.2434 (ptt) cc_final: 0.2074 (pmm) REVERT: K 172 TYR cc_start: 0.7654 (t80) cc_final: 0.6779 (t80) REVERT: K 214 ARG cc_start: 0.6518 (tmm160) cc_final: 0.5515 (tpp80) REVERT: K 313 MET cc_start: 0.8521 (mmm) cc_final: 0.8181 (mmm) REVERT: K 347 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7595 (t) REVERT: N 253 LEU cc_start: 0.9536 (mt) cc_final: 0.9311 (mt) REVERT: N 282 ARG cc_start: 0.6981 (mtp180) cc_final: 0.6333 (mtp85) REVERT: N 309 ARG cc_start: 0.5459 (mtt-85) cc_final: 0.5203 (mtt-85) REVERT: M 24 TYR cc_start: 0.4746 (OUTLIER) cc_final: 0.3234 (t80) REVERT: M 172 TYR cc_start: 0.7600 (t80) cc_final: 0.7349 (t80) REVERT: M 214 ARG cc_start: 0.6490 (tmm160) cc_final: 0.5465 (tpp80) REVERT: M 249 ASN cc_start: 0.7982 (m110) cc_final: 0.7611 (m-40) REVERT: M 313 MET cc_start: 0.8236 (mmm) cc_final: 0.7557 (mmm) REVERT: M 347 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7385 (t) REVERT: M 413 MET cc_start: 0.8235 (tmm) cc_final: 0.7873 (tmm) REVERT: P 14 ASN cc_start: 0.9333 (m-40) cc_final: 0.8865 (m-40) REVERT: P 267 MET cc_start: 0.8491 (ttp) cc_final: 0.8190 (ttt) REVERT: P 282 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6259 (mtp85) REVERT: P 289 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5589 (mp) REVERT: P 293 MET cc_start: 0.8036 (tpp) cc_final: 0.7829 (tpp) REVERT: P 309 ARG cc_start: 0.5228 (mtt-85) cc_final: 0.5007 (mtt-85) REVERT: P 388 MET cc_start: 0.8531 (ttm) cc_final: 0.8006 (ttm) REVERT: O 214 ARG cc_start: 0.5963 (tmm-80) cc_final: 0.5430 (tpp80) REVERT: O 313 MET cc_start: 0.8506 (mmm) cc_final: 0.8092 (tpp) REVERT: O 347 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7659 (t) REVERT: O 413 MET cc_start: 0.8378 (ttp) cc_final: 0.8116 (tmm) REVERT: O 423 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8796 (tp30) REVERT: R 14 ASN cc_start: 0.9344 (m-40) cc_final: 0.8860 (m-40) REVERT: R 282 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6072 (mtp85) REVERT: R 293 MET cc_start: 0.8039 (tpp) cc_final: 0.7688 (tpp) REVERT: Q 24 TYR cc_start: 0.4753 (OUTLIER) cc_final: 0.3351 (t80) REVERT: Q 183 GLU cc_start: 0.8464 (tt0) cc_final: 0.7942 (mm-30) REVERT: Q 259 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8612 (mm) REVERT: Q 347 CYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7544 (t) outliers start: 226 outliers final: 167 residues processed: 1279 average time/residue: 0.5168 time to fit residues: 1164.7739 Evaluate side-chains 1265 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1080 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 286 VAL Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 24 TYR Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 99 ASN Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 274 THR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 147 SER Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 296 PHE Chi-restraints excluded: chain O residue 317 LEU Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 24 TYR Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 190 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 347 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 456 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 440 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 468 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 chunk 364 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 579 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 62100 Z= 0.296 Angle : 0.778 18.365 84528 Z= 0.372 Chirality : 0.047 0.243 9342 Planarity : 0.005 0.061 10989 Dihedral : 18.786 177.562 9117 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.02 % Allowed : 26.57 % Favored : 69.41 % 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: -1.86 (0.10), residues: 7749 helix: -0.16 (0.09), residues: 3159 sheet: -1.32 (0.16), residues: 1053 loop : -2.20 (0.10), residues: 3537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 21 HIS 0.007 0.001 HIS M 107 PHE 0.034 0.002 PHE N 20 TYR 0.026 0.001 TYR A 103 ARG 0.008 0.001 ARG J 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1091 time to evaluate : 5.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9399 (m-40) cc_final: 0.9010 (m-40) REVERT: B 133 PHE cc_start: 0.7860 (m-10) cc_final: 0.7579 (m-10) REVERT: B 198 GLU cc_start: 0.8411 (pm20) cc_final: 0.8174 (pm20) REVERT: B 267 MET cc_start: 0.7738 (ttt) cc_final: 0.7476 (ttt) REVERT: B 293 MET cc_start: 0.7996 (tpp) cc_final: 0.7405 (tpp) REVERT: B 367 PHE cc_start: 0.8717 (t80) cc_final: 0.8199 (t80) REVERT: A 36 MET cc_start: 0.5515 (mpp) cc_final: 0.5215 (mmt) REVERT: A 313 MET cc_start: 0.8458 (mmm) cc_final: 0.8088 (mmm) REVERT: A 347 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7140 (t) REVERT: D 14 ASN cc_start: 0.9382 (m-40) cc_final: 0.8910 (m-40) REVERT: D 108 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: D 134 GLN cc_start: 0.8429 (tp40) cc_final: 0.8135 (tp40) REVERT: D 147 MET cc_start: 0.8076 (mmp) cc_final: 0.7811 (tpp) REVERT: D 282 ARG cc_start: 0.6788 (mtp180) cc_final: 0.5994 (mtp85) REVERT: D 293 MET cc_start: 0.7977 (tpt) cc_final: 0.7589 (tpp) REVERT: D 406 MET cc_start: 0.8538 (mmp) cc_final: 0.8323 (mmp) REVERT: C 36 MET cc_start: 0.5706 (mpp) cc_final: 0.5492 (mmt) REVERT: C 172 TYR cc_start: 0.7877 (t80) cc_final: 0.7007 (t80) REVERT: C 202 PHE cc_start: 0.7503 (m-80) cc_final: 0.7148 (m-80) REVERT: C 288 VAL cc_start: 0.9121 (m) cc_final: 0.8749 (t) REVERT: C 313 MET cc_start: 0.8512 (mmm) cc_final: 0.7615 (mmm) REVERT: C 347 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7566 (t) REVERT: C 373 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6811 (ptp-170) REVERT: C 423 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8861 (tp30) REVERT: F 14 ASN cc_start: 0.9364 (m-40) cc_final: 0.8827 (m-40) REVERT: F 99 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7416 (p0) REVERT: F 108 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: F 147 MET cc_start: 0.8352 (mmt) cc_final: 0.7995 (tpp) REVERT: F 154 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8123 (tttt) REVERT: F 257 MET cc_start: 0.9128 (mmp) cc_final: 0.8871 (mmp) REVERT: F 267 MET cc_start: 0.8504 (ttp) cc_final: 0.7768 (ttm) REVERT: F 282 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6505 (mtp85) REVERT: F 299 MET cc_start: 0.7032 (ptp) cc_final: 0.6475 (pmm) REVERT: F 367 PHE cc_start: 0.8622 (t80) cc_final: 0.8123 (t80) REVERT: F 415 MET cc_start: 0.8513 (tmm) cc_final: 0.8292 (tmm) REVERT: E 313 MET cc_start: 0.8782 (mmm) cc_final: 0.8462 (mmm) REVERT: E 423 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8879 (tp30) REVERT: H 14 ASN cc_start: 0.9400 (m-40) cc_final: 0.8942 (m-40) REVERT: H 198 GLU cc_start: 0.8376 (pm20) cc_final: 0.8148 (pm20) REVERT: H 282 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6231 (mtp85) REVERT: H 388 MET cc_start: 0.8477 (ttm) cc_final: 0.8189 (ttp) REVERT: G 202 PHE cc_start: 0.7409 (m-80) cc_final: 0.6851 (m-80) REVERT: G 225 THR cc_start: 0.4339 (OUTLIER) cc_final: 0.4094 (m) REVERT: G 279 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 296 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5668 (m-80) REVERT: G 313 MET cc_start: 0.8362 (mmm) cc_final: 0.7834 (mmm) REVERT: G 347 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7469 (t) REVERT: G 377 MET cc_start: 0.7369 (mtt) cc_final: 0.6984 (mtp) REVERT: J 14 ASN cc_start: 0.9344 (m-40) cc_final: 0.8711 (m-40) REVERT: J 99 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.6916 (p0) REVERT: J 134 GLN cc_start: 0.8126 (tp40) cc_final: 0.7847 (tp40) REVERT: J 147 MET cc_start: 0.8281 (mmt) cc_final: 0.7797 (tpp) REVERT: J 282 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6868 (mtp85) REVERT: J 309 ARG cc_start: 0.5673 (mtt-85) cc_final: 0.5354 (mtt-85) REVERT: I 225 THR cc_start: 0.3900 (OUTLIER) cc_final: 0.3676 (m) REVERT: I 313 MET cc_start: 0.8565 (mmm) cc_final: 0.7954 (mmm) REVERT: I 347 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7246 (t) REVERT: L 14 ASN cc_start: 0.9378 (m-40) cc_final: 0.8927 (m-40) REVERT: L 253 LEU cc_start: 0.9595 (mt) cc_final: 0.9347 (mt) REVERT: L 293 MET cc_start: 0.8153 (tpp) cc_final: 0.7792 (tpp) REVERT: K 313 MET cc_start: 0.8571 (mmm) cc_final: 0.8260 (mmm) REVERT: K 347 CYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7545 (t) REVERT: K 425 MET cc_start: 0.8693 (mmp) cc_final: 0.8182 (mmt) REVERT: N 253 LEU cc_start: 0.9548 (mt) cc_final: 0.9300 (mt) REVERT: N 282 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6742 (mtp85) REVERT: N 309 ARG cc_start: 0.5373 (mtt-85) cc_final: 0.5119 (mtt-85) REVERT: M 24 TYR cc_start: 0.4608 (OUTLIER) cc_final: 0.3102 (t80) REVERT: M 249 ASN cc_start: 0.8030 (m110) cc_final: 0.7698 (m110) REVERT: M 313 MET cc_start: 0.8404 (mmm) cc_final: 0.7847 (mmm) REVERT: M 347 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7415 (t) REVERT: P 14 ASN cc_start: 0.9380 (m-40) cc_final: 0.8873 (m-40) REVERT: P 282 ARG cc_start: 0.7158 (mtp180) cc_final: 0.6664 (mtp85) REVERT: P 289 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5546 (mp) REVERT: P 293 MET cc_start: 0.7992 (tpp) cc_final: 0.7588 (tpp) REVERT: P 309 ARG cc_start: 0.5338 (mtt-85) cc_final: 0.5062 (mtt-85) REVERT: O 347 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7646 (t) REVERT: O 413 MET cc_start: 0.8342 (ttp) cc_final: 0.8043 (tmm) REVERT: O 423 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8831 (tp30) REVERT: R 14 ASN cc_start: 0.9398 (m-40) cc_final: 0.8873 (m-40) REVERT: R 267 MET cc_start: 0.8163 (ttp) cc_final: 0.7303 (ttt) REVERT: R 282 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6437 (mtp85) REVERT: R 289 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5182 (mp) REVERT: R 293 MET cc_start: 0.8006 (tpp) cc_final: 0.7691 (tpp) REVERT: R 299 MET cc_start: 0.7720 (ptp) cc_final: 0.6949 (pmm) REVERT: R 363 MET cc_start: 0.1048 (ptt) cc_final: 0.0562 (pmm) REVERT: Q 24 TYR cc_start: 0.4862 (OUTLIER) cc_final: 0.3590 (t80) REVERT: Q 259 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8603 (mm) outliers start: 255 outliers final: 202 residues processed: 1253 average time/residue: 0.5058 time to fit residues: 1115.6210 Evaluate side-chains 1271 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1049 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 303 CYS Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 354 CYS Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 76 ASP Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 225 THR Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 354 CYS Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 193 VAL Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 24 TYR Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 238 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 296 PHE Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 274 THR Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 354 CYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 76 ASP Chi-restraints excluded: chain O residue 147 SER Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 234 ILE Chi-restraints excluded: chain O residue 271 THR Chi-restraints excluded: chain O residue 296 PHE Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 303 CYS Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 24 TYR Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 190 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 670 optimal weight: 0.0030 chunk 706 optimal weight: 1.9990 chunk 644 optimal weight: 4.9990 chunk 687 optimal weight: 2.9990 chunk 413 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 539 optimal weight: 2.9990 chunk 210 optimal weight: 0.3980 chunk 620 optimal weight: 0.0060 chunk 649 optimal weight: 0.4980 chunk 684 optimal weight: 9.9990 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 62100 Z= 0.176 Angle : 0.737 17.309 84528 Z= 0.345 Chirality : 0.045 0.224 9342 Planarity : 0.005 0.061 10989 Dihedral : 18.442 179.401 9117 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.93 % Allowed : 28.13 % Favored : 68.94 % 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: -1.52 (0.10), residues: 7749 helix: -0.03 (0.10), residues: 3168 sheet: -1.11 (0.18), residues: 927 loop : -1.87 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 21 HIS 0.006 0.001 HIS E 107 PHE 0.029 0.001 PHE J 133 TYR 0.028 0.001 TYR A 172 ARG 0.005 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1141 time to evaluate : 6.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7879 (m-10) cc_final: 0.7515 (m-10) REVERT: B 267 MET cc_start: 0.7309 (ttt) cc_final: 0.6413 (tmm) REVERT: B 293 MET cc_start: 0.7940 (tpp) cc_final: 0.7662 (tpp) REVERT: A 313 MET cc_start: 0.8268 (mmm) cc_final: 0.7944 (mmm) REVERT: A 347 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7445 (t) REVERT: D 14 ASN cc_start: 0.9342 (m-40) cc_final: 0.8922 (m-40) REVERT: D 134 GLN cc_start: 0.8415 (tp40) cc_final: 0.8104 (tp40) REVERT: D 137 HIS cc_start: 0.8114 (p90) cc_final: 0.7601 (p90) REVERT: D 267 MET cc_start: 0.7481 (ttt) cc_final: 0.7152 (tpp) REVERT: D 274 THR cc_start: 0.6545 (OUTLIER) cc_final: 0.6329 (p) REVERT: D 282 ARG cc_start: 0.6808 (mtp180) cc_final: 0.6231 (mtp85) REVERT: D 293 MET cc_start: 0.7749 (tpt) cc_final: 0.7359 (tpp) REVERT: D 370 ASN cc_start: 0.8332 (t0) cc_final: 0.7437 (t0) REVERT: C 172 TYR cc_start: 0.7671 (t80) cc_final: 0.6866 (t80) REVERT: C 202 PHE cc_start: 0.7306 (m-80) cc_final: 0.7100 (m-80) REVERT: C 302 MET cc_start: 0.8250 (mmp) cc_final: 0.7927 (mmp) REVERT: C 312 TYR cc_start: 0.8393 (m-10) cc_final: 0.8135 (m-10) REVERT: C 313 MET cc_start: 0.8529 (mmm) cc_final: 0.7705 (tpp) REVERT: C 315 CYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7809 (p) REVERT: C 347 CYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7690 (t) REVERT: C 423 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8854 (tp30) REVERT: F 14 ASN cc_start: 0.9367 (m-40) cc_final: 0.8853 (m-40) REVERT: F 99 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7118 (p0) REVERT: F 108 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: F 147 MET cc_start: 0.8262 (mmt) cc_final: 0.7929 (tpp) REVERT: F 267 MET cc_start: 0.8472 (ttp) cc_final: 0.7811 (ttm) REVERT: F 282 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6583 (mtp85) REVERT: F 293 MET cc_start: 0.8033 (tpp) cc_final: 0.7665 (tpp) REVERT: F 299 MET cc_start: 0.6826 (ptp) cc_final: 0.6459 (pmm) REVERT: E 313 MET cc_start: 0.8587 (mmm) cc_final: 0.8212 (mmm) REVERT: E 347 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7798 (t) REVERT: E 423 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8870 (tp30) REVERT: H 14 ASN cc_start: 0.9321 (m-40) cc_final: 0.8999 (m-40) REVERT: H 282 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6202 (mtp85) REVERT: H 299 MET cc_start: 0.7764 (ptp) cc_final: 0.7089 (mpp) REVERT: H 388 MET cc_start: 0.8500 (ttm) cc_final: 0.8104 (ttm) REVERT: G 36 MET cc_start: 0.5292 (mpp) cc_final: 0.5062 (mmt) REVERT: G 202 PHE cc_start: 0.7327 (m-80) cc_final: 0.7000 (m-80) REVERT: G 225 THR cc_start: 0.4073 (OUTLIER) cc_final: 0.3848 (m) REVERT: G 279 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7447 (mm-30) REVERT: G 313 MET cc_start: 0.8394 (mmm) cc_final: 0.8105 (mmm) REVERT: G 347 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7503 (t) REVERT: G 377 MET cc_start: 0.7341 (mtt) cc_final: 0.6951 (mtp) REVERT: J 14 ASN cc_start: 0.9283 (m-40) cc_final: 0.8718 (m-40) REVERT: J 99 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6524 (p0) REVERT: J 134 GLN cc_start: 0.8035 (tp40) cc_final: 0.7541 (tp-100) REVERT: J 137 HIS cc_start: 0.8291 (p90) cc_final: 0.7834 (p90) REVERT: J 147 MET cc_start: 0.8153 (mmt) cc_final: 0.7630 (tpp) REVERT: J 274 THR cc_start: 0.6616 (OUTLIER) cc_final: 0.6355 (p) REVERT: J 282 ARG cc_start: 0.7313 (mtp180) cc_final: 0.7045 (mtp85) REVERT: J 300 MET cc_start: 0.7632 (mpp) cc_final: 0.6651 (pmm) REVERT: J 309 ARG cc_start: 0.5601 (mtt-85) cc_final: 0.5296 (mtt-85) REVERT: J 367 PHE cc_start: 0.7780 (t80) cc_final: 0.6918 (t80) REVERT: J 370 ASN cc_start: 0.8511 (t0) cc_final: 0.7781 (t0) REVERT: I 172 TYR cc_start: 0.7675 (t80) cc_final: 0.6884 (t80) REVERT: I 313 MET cc_start: 0.8606 (mmm) cc_final: 0.7982 (mmm) REVERT: I 347 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7173 (t) REVERT: I 423 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8816 (tp30) REVERT: L 14 ASN cc_start: 0.9319 (m-40) cc_final: 0.8904 (m-40) REVERT: L 147 MET cc_start: 0.8224 (mmt) cc_final: 0.7987 (tpp) REVERT: L 267 MET cc_start: 0.7614 (ttt) cc_final: 0.7148 (ttt) REVERT: L 274 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6537 (p) REVERT: L 293 MET cc_start: 0.8104 (tpp) cc_final: 0.7795 (tpp) REVERT: K 172 TYR cc_start: 0.7420 (t80) cc_final: 0.6620 (t80) REVERT: K 202 PHE cc_start: 0.7252 (m-80) cc_final: 0.6930 (m-80) REVERT: K 313 MET cc_start: 0.8546 (mmm) cc_final: 0.7945 (tpp) REVERT: K 347 CYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7484 (t) REVERT: K 425 MET cc_start: 0.8649 (mmp) cc_final: 0.8094 (mmt) REVERT: N 253 LEU cc_start: 0.9541 (mt) cc_final: 0.9308 (mt) REVERT: N 282 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6577 (mtp85) REVERT: N 299 MET cc_start: 0.7082 (ptp) cc_final: 0.6872 (pmm) REVERT: N 300 MET cc_start: 0.7885 (mpp) cc_final: 0.6458 (pmm) REVERT: N 309 ARG cc_start: 0.5434 (mtt-85) cc_final: 0.5180 (mtt-85) REVERT: M 92 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6856 (mm) REVERT: M 172 TYR cc_start: 0.7468 (t80) cc_final: 0.7130 (t80) REVERT: M 249 ASN cc_start: 0.7926 (m110) cc_final: 0.7563 (m110) REVERT: M 313 MET cc_start: 0.8220 (mmm) cc_final: 0.7481 (mmm) REVERT: M 347 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7298 (t) REVERT: M 413 MET cc_start: 0.7770 (tmm) cc_final: 0.7529 (tmm) REVERT: P 14 ASN cc_start: 0.9328 (m-40) cc_final: 0.8866 (m-40) REVERT: P 124 CYS cc_start: 0.7317 (t) cc_final: 0.6564 (m) REVERT: P 147 MET cc_start: 0.8317 (mmm) cc_final: 0.8028 (mmt) REVERT: P 282 ARG cc_start: 0.7233 (mtp180) cc_final: 0.6529 (mtp85) REVERT: P 289 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5601 (mp) REVERT: P 363 MET cc_start: 0.3476 (pmm) cc_final: 0.3208 (pmm) REVERT: P 386 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8433 (t) REVERT: O 347 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7701 (t) REVERT: O 423 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8842 (tp30) REVERT: R 14 ASN cc_start: 0.9360 (m-40) cc_final: 0.8947 (m-40) REVERT: R 147 MET cc_start: 0.8297 (mmt) cc_final: 0.7758 (tpp) REVERT: R 282 ARG cc_start: 0.6914 (mtp180) cc_final: 0.5968 (mtp85) REVERT: R 289 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4980 (mp) REVERT: R 293 MET cc_start: 0.7906 (tpp) cc_final: 0.7621 (tpp) REVERT: Q 24 TYR cc_start: 0.4587 (OUTLIER) cc_final: 0.3269 (t80) REVERT: Q 36 MET cc_start: 0.5550 (mpp) cc_final: 0.5319 (mmt) REVERT: Q 183 GLU cc_start: 0.8392 (tt0) cc_final: 0.7987 (mm-30) REVERT: Q 259 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (mm) REVERT: Q 347 CYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7613 (t) outliers start: 186 outliers final: 143 residues processed: 1262 average time/residue: 0.5085 time to fit residues: 1125.6002 Evaluate side-chains 1247 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1081 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 99 ASN Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain I residue 69 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 354 CYS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 223 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 354 CYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain P residue 386 THR Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 147 SER Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain O residue 223 THR Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 24 TYR Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 190 THR Chi-restraints excluded: chain Q residue 223 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 451 optimal weight: 0.0000 chunk 726 optimal weight: 3.9990 chunk 443 optimal weight: 0.6980 chunk 344 optimal weight: 0.0470 chunk 505 optimal weight: 0.9980 chunk 762 optimal weight: 0.7980 chunk 701 optimal weight: 0.9980 chunk 606 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 468 optimal weight: 3.9990 chunk 372 optimal weight: 3.9990 overall best weight: 0.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 43 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62100 Z= 0.192 Angle : 0.742 16.898 84528 Z= 0.347 Chirality : 0.045 0.216 9342 Planarity : 0.005 0.066 10989 Dihedral : 18.424 179.278 9117 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.70 % Allowed : 28.54 % Favored : 68.76 % 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: -1.49 (0.10), residues: 7749 helix: 0.01 (0.10), residues: 3168 sheet: -1.05 (0.18), residues: 927 loop : -1.89 (0.10), residues: 3654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 21 HIS 0.005 0.001 HIS G 107 PHE 0.035 0.001 PHE N 20 TYR 0.036 0.001 TYR A 172 ARG 0.005 0.000 ARG D 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15498 Ramachandran restraints generated. 7749 Oldfield, 0 Emsley, 7749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1098 time to evaluate : 5.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASN cc_start: 0.9322 (m-40) cc_final: 0.9012 (m-40) REVERT: B 233 MET cc_start: 0.6713 (ptm) cc_final: 0.6274 (tmm) REVERT: B 267 MET cc_start: 0.7271 (ttt) cc_final: 0.6984 (ttt) REVERT: B 293 MET cc_start: 0.7915 (tpp) cc_final: 0.7351 (tpp) REVERT: B 367 PHE cc_start: 0.8405 (t80) cc_final: 0.8086 (t80) REVERT: A 31 GLN cc_start: 0.7120 (mm110) cc_final: 0.6911 (mm-40) REVERT: A 302 MET cc_start: 0.7863 (mmt) cc_final: 0.7446 (mmp) REVERT: A 313 MET cc_start: 0.8276 (mmm) cc_final: 0.7884 (mmm) REVERT: A 347 CYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7517 (t) REVERT: D 14 ASN cc_start: 0.9369 (m-40) cc_final: 0.8979 (m-40) REVERT: D 134 GLN cc_start: 0.8434 (tp40) cc_final: 0.8083 (tp-100) REVERT: D 137 HIS cc_start: 0.8083 (p90) cc_final: 0.7591 (p90) REVERT: D 282 ARG cc_start: 0.6821 (mtp180) cc_final: 0.6211 (mtp85) REVERT: D 293 MET cc_start: 0.7787 (tpt) cc_final: 0.7294 (tpp) REVERT: D 300 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7055 (pmm) REVERT: D 367 PHE cc_start: 0.7862 (t80) cc_final: 0.6947 (t80) REVERT: D 370 ASN cc_start: 0.8305 (t0) cc_final: 0.7378 (t0) REVERT: C 172 TYR cc_start: 0.7484 (t80) cc_final: 0.6990 (t80) REVERT: C 202 PHE cc_start: 0.7358 (m-80) cc_final: 0.7092 (m-80) REVERT: C 302 MET cc_start: 0.8191 (mmp) cc_final: 0.7886 (mmp) REVERT: C 312 TYR cc_start: 0.8444 (m-10) cc_final: 0.8218 (m-10) REVERT: C 313 MET cc_start: 0.8530 (mmm) cc_final: 0.7763 (tpp) REVERT: C 315 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7719 (p) REVERT: C 347 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7715 (t) REVERT: C 423 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8849 (tp30) REVERT: F 14 ASN cc_start: 0.9323 (m-40) cc_final: 0.8813 (m-40) REVERT: F 99 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.7153 (p0) REVERT: F 108 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: F 124 CYS cc_start: 0.7364 (t) cc_final: 0.6702 (p) REVERT: F 147 MET cc_start: 0.8293 (mmt) cc_final: 0.7963 (tpp) REVERT: F 267 MET cc_start: 0.8443 (ttp) cc_final: 0.7737 (ttm) REVERT: F 282 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6603 (mtp85) REVERT: F 299 MET cc_start: 0.6918 (ptp) cc_final: 0.6458 (pmm) REVERT: F 321 MET cc_start: 0.6527 (tmm) cc_final: 0.5789 (tmm) REVERT: E 313 MET cc_start: 0.8661 (mmm) cc_final: 0.8305 (mmm) REVERT: E 423 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8831 (tp30) REVERT: H 14 ASN cc_start: 0.9323 (m-40) cc_final: 0.8977 (m-40) REVERT: H 124 CYS cc_start: 0.7603 (t) cc_final: 0.7036 (p) REVERT: H 282 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6351 (mtp85) REVERT: H 299 MET cc_start: 0.7815 (ptp) cc_final: 0.7112 (mpp) REVERT: H 388 MET cc_start: 0.8488 (ttm) cc_final: 0.8098 (ttm) REVERT: G 202 PHE cc_start: 0.7317 (m-80) cc_final: 0.6988 (m-80) REVERT: G 225 THR cc_start: 0.4139 (OUTLIER) cc_final: 0.3934 (m) REVERT: G 313 MET cc_start: 0.8230 (mmm) cc_final: 0.7936 (mmm) REVERT: G 347 CYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7612 (t) REVERT: G 377 MET cc_start: 0.7221 (mtt) cc_final: 0.6828 (mtp) REVERT: J 14 ASN cc_start: 0.9361 (m-40) cc_final: 0.8896 (m-40) REVERT: J 124 CYS cc_start: 0.7793 (t) cc_final: 0.7177 (p) REVERT: J 134 GLN cc_start: 0.8044 (tp40) cc_final: 0.7774 (tp40) REVERT: J 137 HIS cc_start: 0.8254 (p90) cc_final: 0.7816 (p90) REVERT: J 147 MET cc_start: 0.8190 (mmt) cc_final: 0.7661 (tpp) REVERT: J 274 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.6358 (p) REVERT: J 282 ARG cc_start: 0.7286 (mtp180) cc_final: 0.6972 (mtp85) REVERT: J 300 MET cc_start: 0.7593 (mpp) cc_final: 0.6598 (pmm) REVERT: J 309 ARG cc_start: 0.5710 (mtt-85) cc_final: 0.5411 (mtt-85) REVERT: J 367 PHE cc_start: 0.7792 (t80) cc_final: 0.7010 (t80) REVERT: J 370 ASN cc_start: 0.8418 (t0) cc_final: 0.7661 (t0) REVERT: I 172 TYR cc_start: 0.7761 (t80) cc_final: 0.6880 (t80) REVERT: I 313 MET cc_start: 0.8632 (mmm) cc_final: 0.7988 (mmm) REVERT: I 347 CYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7253 (t) REVERT: I 423 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8809 (tp30) REVERT: L 14 ASN cc_start: 0.9335 (m-40) cc_final: 0.8979 (m-40) REVERT: L 147 MET cc_start: 0.8234 (mmt) cc_final: 0.8000 (tpp) REVERT: L 253 LEU cc_start: 0.9573 (mt) cc_final: 0.9364 (mt) REVERT: L 274 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6567 (p) REVERT: L 293 MET cc_start: 0.8103 (tpp) cc_final: 0.7762 (tpp) REVERT: K 172 TYR cc_start: 0.7431 (t80) cc_final: 0.6602 (t80) REVERT: K 202 PHE cc_start: 0.7283 (m-80) cc_final: 0.6967 (m-80) REVERT: K 313 MET cc_start: 0.8558 (mmm) cc_final: 0.8007 (tpp) REVERT: K 347 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7499 (t) REVERT: K 377 MET cc_start: 0.6710 (mtp) cc_final: 0.6262 (mtp) REVERT: K 413 MET cc_start: 0.7816 (tmm) cc_final: 0.7615 (tmm) REVERT: N 124 CYS cc_start: 0.7695 (t) cc_final: 0.7047 (p) REVERT: N 147 MET cc_start: 0.8367 (mmp) cc_final: 0.7723 (tpp) REVERT: N 253 LEU cc_start: 0.9554 (mt) cc_final: 0.9321 (mt) REVERT: N 282 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6728 (mtp85) REVERT: N 299 MET cc_start: 0.7134 (ptp) cc_final: 0.6756 (pmm) REVERT: M 172 TYR cc_start: 0.7516 (t80) cc_final: 0.7268 (t80) REVERT: M 249 ASN cc_start: 0.7906 (m110) cc_final: 0.7660 (m110) REVERT: M 313 MET cc_start: 0.8237 (mmm) cc_final: 0.7417 (mmm) REVERT: M 347 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7337 (t) REVERT: M 413 MET cc_start: 0.7675 (tmm) cc_final: 0.7448 (tmm) REVERT: P 14 ASN cc_start: 0.9410 (m-40) cc_final: 0.8936 (m-40) REVERT: P 124 CYS cc_start: 0.7297 (t) cc_final: 0.6602 (p) REVERT: P 147 MET cc_start: 0.8382 (mmm) cc_final: 0.8156 (mmt) REVERT: P 267 MET cc_start: 0.8322 (ttp) cc_final: 0.8106 (ttt) REVERT: P 282 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6618 (mtp85) REVERT: P 289 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5521 (mp) REVERT: P 363 MET cc_start: 0.3522 (pmm) cc_final: 0.3179 (pmm) REVERT: O 347 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7806 (t) REVERT: O 423 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8842 (tp30) REVERT: R 14 ASN cc_start: 0.9381 (m-40) cc_final: 0.8860 (m-40) REVERT: R 147 MET cc_start: 0.8377 (mmt) cc_final: 0.7833 (tpp) REVERT: R 267 MET cc_start: 0.7919 (ttp) cc_final: 0.7098 (ttt) REVERT: R 282 ARG cc_start: 0.6982 (mtp180) cc_final: 0.6575 (mtp85) REVERT: R 289 LEU cc_start: 0.5227 (OUTLIER) cc_final: 0.4972 (mp) REVERT: R 293 MET cc_start: 0.7938 (tpp) cc_final: 0.7651 (tpp) REVERT: Q 183 GLU cc_start: 0.8473 (tt0) cc_final: 0.8018 (mm-30) REVERT: Q 259 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8618 (mm) REVERT: Q 347 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7586 (t) outliers start: 171 outliers final: 142 residues processed: 1208 average time/residue: 0.5073 time to fit residues: 1077.8751 Evaluate side-chains 1232 residues out of total 6624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1072 time to evaluate : 5.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 101 TRP Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 99 ASN Chi-restraints excluded: chain H residue 101 TRP Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain H residue 225 LEU Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain H residue 386 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 223 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 238 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain J residue 101 TRP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain J residue 219 THR Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 354 CYS Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 147 SER Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 226 ASN Chi-restraints excluded: chain I residue 238 ILE Chi-restraints excluded: chain I residue 271 THR Chi-restraints excluded: chain I residue 347 CYS Chi-restraints excluded: chain L residue 101 TRP Chi-restraints excluded: chain L residue 136 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 219 THR Chi-restraints excluded: chain L residue 225 LEU Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 274 THR Chi-restraints excluded: chain L residue 331 LEU Chi-restraints excluded: chain L residue 354 CYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 226 ASN Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 347 CYS Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 99 ASN Chi-restraints excluded: chain N residue 101 TRP Chi-restraints excluded: chain N residue 136 THR Chi-restraints excluded: chain N residue 166 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain N residue 303 CYS Chi-restraints excluded: chain N residue 331 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 226 ASN Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain M residue 347 CYS Chi-restraints excluded: chain P residue 101 TRP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 258 VAL Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 303 CYS Chi-restraints excluded: chain P residue 331 LEU Chi-restraints excluded: chain P residue 354 CYS Chi-restraints excluded: chain P residue 377 LEU Chi-restraints excluded: chain O residue 7 ILE Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 147 SER Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 190 THR Chi-restraints excluded: chain O residue 226 ASN Chi-restraints excluded: chain O residue 347 CYS Chi-restraints excluded: chain O residue 368 LEU Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 101 TRP Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 353 VAL Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain Q residue 7 ILE Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 189 LEU Chi-restraints excluded: chain Q residue 190 THR Chi-restraints excluded: chain Q residue 226 ASN Chi-restraints excluded: chain Q residue 234 ILE Chi-restraints excluded: chain Q residue 238 ILE Chi-restraints excluded: chain Q residue 259 LEU Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 765 random chunks: chunk 482 optimal weight: 3.9990 chunk 646 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 559 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 607 optimal weight: 0.9990 chunk 254 optimal weight: 0.9990 chunk 624 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 15 GLN ** M 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 370 ASN ** P 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN ** O 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** R 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.133195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.110657 restraints weight = 173633.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.114255 restraints weight = 100924.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.116738 restraints weight = 68649.213| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 62100 Z= 0.227 Angle : 0.753 16.990 84528 Z= 0.353 Chirality : 0.045 0.327 9342 Planarity : 0.005 0.059 10989 Dihedral : 18.410 179.814 9117 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.81 % Allowed : 28.53 % Favored : 68.67 % 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: -1.53 (0.10), residues: 7749 helix: 0.02 (0.10), residues: 3150 sheet: -1.15 (0.17), residues: 936 loop : -1.91 (0.10), residues: 3663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 21 HIS 0.005 0.001 HIS G 107 PHE 0.030 0.001 PHE N 20 TYR 0.043 0.001 TYR A 172 ARG 0.006 0.000 ARG E 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16845.47 seconds wall clock time: 296 minutes 10.84 seconds (17770.84 seconds total)