Starting phenix.real_space_refine on Tue Mar 19 10:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tsv_10566/03_2024/6tsv_10566.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 14952 2.51 5 N 4008 2.21 5 O 4824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P ARG 31": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q ARG 31": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "R ARG 28": "NH1" <-> "NH2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ARG 51": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 51": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T ARG 51": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 80": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 31": "NH1" <-> "NH2" Residue "U ARG 51": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" Residue "V ARG 31": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ARG 80": "NH1" <-> "NH2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 80": "NH1" <-> "NH2" Residue "X ARG 28": "NH1" <-> "NH2" Residue "X ARG 31": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "A" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "D" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "F" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "I" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "J" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "K" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "L" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "M" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "N" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "P" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "R" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "S" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "T" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "U" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "W" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "X" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Time building chain proxies: 12.12, per 1000 atoms: 0.51 Number of scatterers: 23832 At special positions: 0 Unit cell: (100.985, 100.985, 173.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4824 8.00 N 4008 7.00 C 14952 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: 9.56 Conformation dependent library (CDL) restraints added in 4.6 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 13.4% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP B 8 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP A 8 " --> pdb=" O ASN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP C 8 " --> pdb=" O ASN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP D 8 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP E 8 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 84 " --> pdb=" O ARG E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP F 8 " --> pdb=" O ASN F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE F 82 " --> pdb=" O ARG F 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 84 " --> pdb=" O ARG F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP G 8 " --> pdb=" O ASN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP H 8 " --> pdb=" O ASN H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 removed outlier: 3.669A pdb=" N ASP I 8 " --> pdb=" O ASN I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE I 83 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP J 8 " --> pdb=" O ASN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE J 83 " --> pdb=" O ALA J 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP K 8 " --> pdb=" O ASN K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP L 8 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE L 84 " --> pdb=" O ARG L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP M 8 " --> pdb=" O ASN M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE M 84 " --> pdb=" O ARG M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP N 8 " --> pdb=" O ASN N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP O 8 " --> pdb=" O ASN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE O 82 " --> pdb=" O ARG O 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE O 84 " --> pdb=" O ARG O 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP P 8 " --> pdb=" O ASN P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE P 82 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE P 83 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 84 " --> pdb=" O ARG P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP Q 8 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE Q 82 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP R 8 " --> pdb=" O ASN R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP S 8 " --> pdb=" O ASN S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE S 82 " --> pdb=" O ARG S 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE S 83 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP T 8 " --> pdb=" O ASN T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE T 83 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE T 84 " --> pdb=" O ARG T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.669A pdb=" N ASP U 8 " --> pdb=" O ASN U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE U 82 " --> pdb=" O ARG U 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE U 83 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE U 84 " --> pdb=" O ARG U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP V 8 " --> pdb=" O ASN V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE V 82 " --> pdb=" O ARG V 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE V 83 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE V 84 " --> pdb=" O ARG V 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP W 8 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.653A pdb=" N ILE W 82 " --> pdb=" O ARG W 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE W 83 " --> pdb=" O ALA W 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE W 84 " --> pdb=" O ARG W 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 9 removed outlier: 3.670A pdb=" N ASP X 8 " --> pdb=" O ASN X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 85 removed outlier: 3.652A pdb=" N ILE X 82 " --> pdb=" O ARG X 78 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE X 83 " --> pdb=" O ALA X 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE X 84 " --> pdb=" O ARG X 80 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP B 14 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 90 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 107 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA B 62 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 69 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 27 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP B 14 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU B 90 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP A 14 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 90 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE A 107 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA A 62 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 69 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 27 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP A 14 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU A 90 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP C 14 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU C 90 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE C 107 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA C 127 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA C 62 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 69 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU C 27 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP C 14 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU C 90 " --> pdb=" O ASP C 14 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP D 14 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU D 90 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE D 107 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA D 127 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA D 62 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL D 69 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU D 27 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP D 14 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU D 90 " --> pdb=" O ASP D 14 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP E 14 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU E 90 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE E 107 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA E 127 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA E 62 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL E 69 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU E 27 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP E 14 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU E 90 " --> pdb=" O ASP E 14 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP F 14 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU F 90 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE F 107 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA F 127 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA F 62 " --> pdb=" O SER F 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL F 69 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU F 27 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP F 14 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU F 90 " --> pdb=" O ASP F 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP G 14 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU G 90 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G 69 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU G 27 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP G 14 " --> pdb=" O GLU G 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU G 90 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP H 14 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU H 90 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE H 107 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA H 127 " --> pdb=" O ILE H 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA H 62 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL H 69 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU H 27 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP H 14 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU H 90 " --> pdb=" O ASP H 14 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP I 14 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU I 90 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE I 107 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA I 127 " --> pdb=" O ILE I 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA I 62 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 69 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU I 27 " --> pdb=" O VAL I 69 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP I 14 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU I 90 " --> pdb=" O ASP I 14 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP J 14 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU J 90 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE J 107 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA J 127 " --> pdb=" O ILE J 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA J 62 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL J 69 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU J 27 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP J 14 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU J 90 " --> pdb=" O ASP J 14 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP K 14 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU K 90 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE K 107 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA K 127 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA K 62 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL K 69 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU K 27 " --> pdb=" O VAL K 69 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP K 14 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU K 90 " --> pdb=" O ASP K 14 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP L 14 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU L 90 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE L 107 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA L 127 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA L 62 " --> pdb=" O SER L 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL L 69 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU L 27 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP L 14 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU L 90 " --> pdb=" O ASP L 14 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP M 14 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU M 90 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE M 107 " --> pdb=" O ALA M 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA M 127 " --> pdb=" O ILE M 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA M 62 " --> pdb=" O SER M 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL M 69 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU M 27 " --> pdb=" O VAL M 69 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP M 14 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU M 90 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP N 14 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU N 90 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL N 69 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU N 27 " --> pdb=" O VAL N 69 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP N 14 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU N 90 " --> pdb=" O ASP N 14 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP O 14 " --> pdb=" O GLU O 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU O 90 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE O 107 " --> pdb=" O ALA O 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA O 127 " --> pdb=" O ILE O 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA O 62 " --> pdb=" O SER O 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL O 69 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU O 27 " --> pdb=" O VAL O 69 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP O 14 " --> pdb=" O GLU O 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU O 90 " --> pdb=" O ASP O 14 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP P 14 " --> pdb=" O GLU P 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU P 90 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE P 107 " --> pdb=" O ALA P 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA P 127 " --> pdb=" O ILE P 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA P 62 " --> pdb=" O SER P 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL P 69 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU P 27 " --> pdb=" O VAL P 69 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP P 14 " --> pdb=" O GLU P 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU P 90 " --> pdb=" O ASP P 14 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU Q 90 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE Q 107 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA Q 127 " --> pdb=" O ILE Q 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA Q 62 " --> pdb=" O SER Q 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL Q 69 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU Q 27 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU Q 90 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP R 14 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU R 90 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE R 107 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA R 127 " --> pdb=" O ILE R 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA R 62 " --> pdb=" O SER R 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL R 69 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU R 27 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP R 14 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU R 90 " --> pdb=" O ASP R 14 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP S 14 " --> pdb=" O GLU S 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU S 90 " --> pdb=" O ASP S 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE S 107 " --> pdb=" O ALA S 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA S 127 " --> pdb=" O ILE S 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA S 62 " --> pdb=" O SER S 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL S 69 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU S 27 " --> pdb=" O VAL S 69 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP S 14 " --> pdb=" O GLU S 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU S 90 " --> pdb=" O ASP S 14 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP T 14 " --> pdb=" O GLU T 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU T 90 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE T 107 " --> pdb=" O ALA T 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA T 127 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA T 62 " --> pdb=" O SER T 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL T 69 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU T 27 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP T 14 " --> pdb=" O GLU T 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU T 90 " --> pdb=" O ASP T 14 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP U 14 " --> pdb=" O GLU U 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU U 90 " --> pdb=" O ASP U 14 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL U 69 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU U 27 " --> pdb=" O VAL U 69 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP U 14 " --> pdb=" O GLU U 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU U 90 " --> pdb=" O ASP U 14 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP V 14 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU V 90 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE V 107 " --> pdb=" O ALA V 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA V 127 " --> pdb=" O ILE V 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA V 62 " --> pdb=" O SER V 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL V 69 " --> pdb=" O LEU V 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU V 27 " --> pdb=" O VAL V 69 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP V 14 " --> pdb=" O GLU V 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU V 90 " --> pdb=" O ASP V 14 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP W 14 " --> pdb=" O GLU W 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU W 90 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE W 107 " --> pdb=" O ALA W 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA W 127 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA W 62 " --> pdb=" O SER W 128 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 69 " --> pdb=" O LEU W 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU W 27 " --> pdb=" O VAL W 69 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 21 through 23 removed outlier: 3.883A pdb=" N ASP W 14 " --> pdb=" O GLU W 90 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU W 90 " --> pdb=" O ASP W 14 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'X' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP X 14 " --> pdb=" O GLU X 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU X 90 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE X 107 " --> pdb=" O ALA X 127 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA X 127 " --> pdb=" O ILE X 107 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA X 62 " --> pdb=" O SER X 128 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL X 69 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU X 27 " --> pdb=" O VAL X 69 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 21 through 23 removed outlier: 3.882A pdb=" N ASP X 14 " --> pdb=" O GLU X 90 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU X 90 " --> pdb=" O ASP X 14 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 2664 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: 9.24 Time building geometry restraints manager: 10.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7994 1.33 - 1.45: 3060 1.45 - 1.56: 13066 1.56 - 1.67: 0 1.67 - 1.79: 96 Bond restraints: 24216 Sorted by residual: bond pdb=" CB ILE G 82 " pdb=" CG2 ILE G 82 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB ILE S 82 " pdb=" CG2 ILE S 82 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB ILE K 82 " pdb=" CG2 ILE K 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CB ILE W 82 " pdb=" CG2 ILE W 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CB ILE C 82 " pdb=" CG2 ILE C 82 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.68e+00 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.26: 312 105.26 - 112.43: 11374 112.43 - 119.60: 8548 119.60 - 126.77: 12286 126.77 - 133.93: 192 Bond angle restraints: 32712 Sorted by residual: angle pdb=" N ILE J 95 " pdb=" CA ILE J 95 " pdb=" C ILE J 95 " ideal model delta sigma weight residual 108.95 103.71 5.24 9.80e-01 1.04e+00 2.86e+01 angle pdb=" N ILE V 95 " pdb=" CA ILE V 95 " pdb=" C ILE V 95 " ideal model delta sigma weight residual 108.95 103.71 5.24 9.80e-01 1.04e+00 2.86e+01 angle pdb=" N ILE M 95 " pdb=" CA ILE M 95 " pdb=" C ILE M 95 " ideal model delta sigma weight residual 108.95 103.73 5.22 9.80e-01 1.04e+00 2.84e+01 angle pdb=" N ILE B 95 " pdb=" CA ILE B 95 " pdb=" C ILE B 95 " ideal model delta sigma weight residual 108.95 103.73 5.22 9.80e-01 1.04e+00 2.84e+01 angle pdb=" N ILE A 95 " pdb=" CA ILE A 95 " pdb=" C ILE A 95 " ideal model delta sigma weight residual 108.95 103.74 5.21 9.80e-01 1.04e+00 2.83e+01 ... (remaining 32707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.71: 11008 8.71 - 17.42: 2192 17.42 - 26.13: 456 26.13 - 34.84: 336 34.84 - 43.55: 120 Dihedral angle restraints: 14112 sinusoidal: 5256 harmonic: 8856 Sorted by residual: dihedral pdb=" CA ILE W 95 " pdb=" C ILE W 95 " pdb=" N PRO W 96 " pdb=" CA PRO W 96 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE K 95 " pdb=" C ILE K 95 " pdb=" N PRO K 96 " pdb=" CA PRO K 96 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE I 95 " pdb=" C ILE I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 14109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2736 0.075 - 0.150: 618 0.150 - 0.225: 222 0.225 - 0.300: 48 0.300 - 0.375: 24 Chirality restraints: 3648 Sorted by residual: chirality pdb=" CB ILE R 107 " pdb=" CA ILE R 107 " pdb=" CG1 ILE R 107 " pdb=" CG2 ILE R 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE F 107 " pdb=" CA ILE F 107 " pdb=" CG1 ILE F 107 " pdb=" CG2 ILE F 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE L 107 " pdb=" CA ILE L 107 " pdb=" CG1 ILE L 107 " pdb=" CG2 ILE L 107 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3645 not shown) Planarity restraints: 4368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 72 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP F 72 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP F 72 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP F 72 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 72 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP R 72 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP R 72 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP R 72 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 72 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" CG ASP K 72 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP K 72 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP K 72 " 0.013 2.00e-02 2.50e+03 ... (remaining 4365 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8590 2.85 - 3.36: 21838 3.36 - 3.87: 41198 3.87 - 4.39: 46320 4.39 - 4.90: 83076 Nonbonded interactions: 201022 Sorted by model distance: nonbonded pdb=" O GLY A 48 " pdb=" NH2 ARG F 60 " model vdw 2.334 2.520 nonbonded pdb=" O GLY N 48 " pdb=" NH2 ARG R 60 " model vdw 2.334 2.520 nonbonded pdb=" O GLY J 48 " pdb=" NH2 ARG N 60 " model vdw 2.334 2.520 nonbonded pdb=" NH2 ARG A 60 " pdb=" O GLY V 48 " model vdw 2.334 2.520 nonbonded pdb=" O GLY R 48 " pdb=" NH2 ARG V 60 " model vdw 2.334 2.520 ... (remaining 201017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 4.770 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 65.270 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.240 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.011 0.064 24216 Z= 0.715 Angle : 1.201 8.801 32712 Z= 0.656 Chirality : 0.080 0.375 3648 Planarity : 0.006 0.049 4368 Dihedral : 11.726 43.550 8496 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.12), residues: 3168 helix: -5.02 (0.04), residues: 480 sheet: -1.48 (0.16), residues: 864 loop : -3.27 (0.12), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP G 50 HIS 0.012 0.008 HIS L 116 PHE 0.022 0.005 PHE U 98 TYR 0.013 0.004 TYR Q 112 ARG 0.015 0.003 ARG X 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1136 time to evaluate : 2.436 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: B 10 LEU cc_start: 0.9070 (mp) cc_final: 0.8843 (mt) REVERT: B 111 ASP cc_start: 0.8525 (p0) cc_final: 0.8176 (p0) REVERT: A 28 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7648 (mmp-170) REVERT: A 91 PHE cc_start: 0.8484 (m-80) cc_final: 0.8277 (m-80) REVERT: C 14 ASP cc_start: 0.7637 (m-30) cc_final: 0.7241 (m-30) REVERT: C 18 SER cc_start: 0.8268 (p) cc_final: 0.7998 (p) REVERT: C 60 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7320 (mtm180) REVERT: D 12 LYS cc_start: 0.8785 (mttp) cc_final: 0.8488 (mtpp) REVERT: D 14 ASP cc_start: 0.7399 (m-30) cc_final: 0.7146 (m-30) REVERT: D 65 SER cc_start: 0.8538 (t) cc_final: 0.8254 (p) REVERT: D 71 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8533 (mtmm) REVERT: D 76 ASP cc_start: 0.8257 (t0) cc_final: 0.8012 (t0) REVERT: E 111 ASP cc_start: 0.8364 (p0) cc_final: 0.7965 (p0) REVERT: F 4 GLN cc_start: 0.8460 (tp40) cc_final: 0.8149 (mm-40) REVERT: F 12 LYS cc_start: 0.8442 (mttp) cc_final: 0.8100 (mmmm) REVERT: F 28 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7483 (mmp-170) REVERT: H 4 GLN cc_start: 0.8793 (tp40) cc_final: 0.8345 (mm-40) REVERT: H 14 ASP cc_start: 0.7278 (m-30) cc_final: 0.7001 (m-30) REVERT: H 15 LEU cc_start: 0.8419 (mm) cc_final: 0.7437 (mm) REVERT: H 23 THR cc_start: 0.8705 (m) cc_final: 0.8499 (p) REVERT: H 44 LEU cc_start: 0.8845 (tm) cc_final: 0.8605 (tp) REVERT: H 50 TRP cc_start: 0.8899 (m100) cc_final: 0.7492 (m100) REVERT: H 65 SER cc_start: 0.8676 (t) cc_final: 0.8371 (p) REVERT: H 92 GLN cc_start: 0.8497 (tt0) cc_final: 0.8249 (tt0) REVERT: H 117 ASN cc_start: 0.9370 (p0) cc_final: 0.9076 (p0) REVERT: I 60 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7587 (mtm110) REVERT: I 111 ASP cc_start: 0.8544 (p0) cc_final: 0.6828 (p0) REVERT: J 12 LYS cc_start: 0.8419 (mttp) cc_final: 0.7971 (mmmm) REVERT: J 28 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7683 (mmp-170) REVERT: J 52 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7688 (mt-10) REVERT: J 71 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8878 (mtpp) REVERT: J 90 GLU cc_start: 0.8020 (tp30) cc_final: 0.7689 (tp30) REVERT: J 109 SER cc_start: 0.8867 (t) cc_final: 0.8659 (m) REVERT: K 14 ASP cc_start: 0.7870 (m-30) cc_final: 0.7273 (m-30) REVERT: K 18 SER cc_start: 0.8248 (p) cc_final: 0.7981 (p) REVERT: K 92 GLN cc_start: 0.8753 (tt0) cc_final: 0.8502 (tt0) REVERT: K 111 ASP cc_start: 0.8278 (p0) cc_final: 0.7928 (p0) REVERT: K 115 SER cc_start: 0.8782 (m) cc_final: 0.8393 (p) REVERT: L 23 THR cc_start: 0.8799 (m) cc_final: 0.8464 (p) REVERT: L 65 SER cc_start: 0.8559 (t) cc_final: 0.8224 (p) REVERT: M 10 LEU cc_start: 0.9066 (mp) cc_final: 0.8843 (mt) REVERT: M 111 ASP cc_start: 0.8540 (p0) cc_final: 0.8171 (p0) REVERT: N 28 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7648 (mmp-170) REVERT: N 91 PHE cc_start: 0.8480 (m-80) cc_final: 0.8272 (m-80) REVERT: O 14 ASP cc_start: 0.7649 (m-30) cc_final: 0.7255 (m-30) REVERT: O 18 SER cc_start: 0.8270 (p) cc_final: 0.8003 (p) REVERT: O 60 ARG cc_start: 0.7597 (mtm-85) cc_final: 0.7335 (mtm180) REVERT: P 12 LYS cc_start: 0.8793 (mttp) cc_final: 0.8483 (mtpp) REVERT: P 14 ASP cc_start: 0.7393 (m-30) cc_final: 0.7139 (m-30) REVERT: P 23 THR cc_start: 0.8886 (m) cc_final: 0.8684 (p) REVERT: P 65 SER cc_start: 0.8538 (t) cc_final: 0.8249 (p) REVERT: P 76 ASP cc_start: 0.8252 (t0) cc_final: 0.8021 (t0) REVERT: Q 111 ASP cc_start: 0.8362 (p0) cc_final: 0.7967 (p0) REVERT: R 4 GLN cc_start: 0.8458 (tp40) cc_final: 0.8152 (mm-40) REVERT: R 12 LYS cc_start: 0.8444 (mttp) cc_final: 0.8100 (mmmm) REVERT: R 28 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7482 (mmp-170) REVERT: S 69 VAL cc_start: 0.9489 (m) cc_final: 0.9283 (p) REVERT: T 4 GLN cc_start: 0.8791 (tp40) cc_final: 0.8344 (mm-40) REVERT: T 14 ASP cc_start: 0.7266 (m-30) cc_final: 0.7004 (m-30) REVERT: T 15 LEU cc_start: 0.8415 (mm) cc_final: 0.7432 (mm) REVERT: T 23 THR cc_start: 0.8706 (m) cc_final: 0.8499 (p) REVERT: T 44 LEU cc_start: 0.8848 (tm) cc_final: 0.8610 (tp) REVERT: T 50 TRP cc_start: 0.8900 (m100) cc_final: 0.7500 (m100) REVERT: T 65 SER cc_start: 0.8678 (t) cc_final: 0.8374 (p) REVERT: T 92 GLN cc_start: 0.8504 (tt0) cc_final: 0.8248 (tt0) REVERT: T 117 ASN cc_start: 0.9372 (p0) cc_final: 0.9080 (p0) REVERT: U 60 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7591 (mtm110) REVERT: U 111 ASP cc_start: 0.8530 (p0) cc_final: 0.6815 (p0) REVERT: V 12 LYS cc_start: 0.8417 (mttp) cc_final: 0.7971 (mmmm) REVERT: V 28 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7682 (mmp-170) REVERT: V 52 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7701 (mt-10) REVERT: V 71 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8881 (mtpp) REVERT: V 90 GLU cc_start: 0.8019 (tp30) cc_final: 0.7686 (tp30) REVERT: V 109 SER cc_start: 0.8864 (t) cc_final: 0.8655 (m) REVERT: W 14 ASP cc_start: 0.7873 (m-30) cc_final: 0.7279 (m-30) REVERT: W 18 SER cc_start: 0.8247 (p) cc_final: 0.7982 (p) REVERT: W 92 GLN cc_start: 0.8750 (tt0) cc_final: 0.8504 (tt0) REVERT: W 111 ASP cc_start: 0.8275 (p0) cc_final: 0.7942 (p0) REVERT: W 115 SER cc_start: 0.8796 (m) cc_final: 0.8409 (p) REVERT: X 23 THR cc_start: 0.8793 (m) cc_final: 0.8461 (p) REVERT: X 50 TRP cc_start: 0.8953 (m100) cc_final: 0.8208 (m100) REVERT: X 65 SER cc_start: 0.8563 (t) cc_final: 0.8230 (p) outliers start: 0 outliers final: 0 residues processed: 1136 average time/residue: 0.3392 time to fit residues: 595.3847 Evaluate side-chains 810 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 283 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS C 92 GLN D 20 GLN D 92 GLN E 47 GLN E 102 GLN E 116 HIS F 20 GLN G 92 GLN H 102 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 GLN L 102 GLN M 116 HIS O 92 GLN P 20 GLN P 92 GLN P 102 GLN Q 47 GLN Q 102 GLN Q 116 HIS R 20 GLN S 92 GLN T 102 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN ** U 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 116 HIS ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 92 GLN X 102 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24216 Z= 0.220 Angle : 0.721 7.170 32712 Z= 0.377 Chirality : 0.051 0.287 3648 Planarity : 0.004 0.038 4368 Dihedral : 6.151 28.683 3384 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.95 % Allowed : 16.09 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.13), residues: 3168 helix: -4.08 (0.09), residues: 480 sheet: -1.13 (0.14), residues: 1176 loop : -2.67 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 50 HIS 0.008 0.002 HIS T 116 PHE 0.034 0.002 PHE P 21 TYR 0.017 0.001 TYR J 122 ARG 0.006 0.001 ARG D 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 951 time to evaluate : 2.703 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: B 7 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8095 (mtpp) REVERT: B 12 LYS cc_start: 0.8634 (mttp) cc_final: 0.8273 (mtpp) REVERT: B 70 PHE cc_start: 0.9295 (t80) cc_final: 0.8720 (t80) REVERT: B 76 ASP cc_start: 0.8308 (t0) cc_final: 0.7950 (t0) REVERT: B 90 GLU cc_start: 0.8066 (tp30) cc_final: 0.7754 (mm-30) REVERT: B 98 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: B 111 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (p0) REVERT: B 123 GLU cc_start: 0.7052 (mp0) cc_final: 0.6753 (mp0) REVERT: B 126 MET cc_start: 0.7935 (mtp) cc_final: 0.6834 (mtp) REVERT: A 4 GLN cc_start: 0.8486 (tp40) cc_final: 0.7969 (mm-40) REVERT: A 12 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7752 (mmmm) REVERT: A 14 ASP cc_start: 0.7635 (m-30) cc_final: 0.6932 (m-30) REVERT: A 28 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7324 (mmp-170) REVERT: A 78 ARG cc_start: 0.8913 (tpt170) cc_final: 0.8468 (tpt90) REVERT: A 85 ASP cc_start: 0.8035 (p0) cc_final: 0.7768 (p0) REVERT: C 12 LYS cc_start: 0.8769 (mttp) cc_final: 0.8330 (mtpp) REVERT: C 60 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7412 (mtm180) REVERT: C 98 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: E 52 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 98 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: E 126 MET cc_start: 0.7508 (mtp) cc_final: 0.7108 (mtp) REVERT: F 4 GLN cc_start: 0.8501 (tp40) cc_final: 0.8176 (tp40) REVERT: F 27 LEU cc_start: 0.9299 (pt) cc_final: 0.9097 (pt) REVERT: F 28 ARG cc_start: 0.8083 (mtm180) cc_final: 0.7262 (mmp-170) REVERT: F 71 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8511 (mtmm) REVERT: F 90 GLU cc_start: 0.8492 (tp30) cc_final: 0.8148 (tp30) REVERT: F 123 GLU cc_start: 0.7508 (mp0) cc_final: 0.7287 (mp0) REVERT: G 60 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7349 (mtm180) REVERT: G 98 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7985 (m-10) REVERT: H 4 GLN cc_start: 0.8677 (tp40) cc_final: 0.8460 (mm-40) REVERT: H 22 GLU cc_start: 0.7078 (mp0) cc_final: 0.6625 (mp0) REVERT: H 23 THR cc_start: 0.8722 (m) cc_final: 0.8324 (p) REVERT: H 44 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (tp) REVERT: H 47 GLN cc_start: 0.7979 (mp10) cc_final: 0.7625 (pm20) REVERT: H 50 TRP cc_start: 0.8316 (m100) cc_final: 0.8030 (m100) REVERT: I 14 ASP cc_start: 0.7369 (m-30) cc_final: 0.7128 (m-30) REVERT: I 35 ASN cc_start: 0.8528 (m-40) cc_final: 0.8257 (m-40) REVERT: I 76 ASP cc_start: 0.8664 (t0) cc_final: 0.8134 (t0) REVERT: I 90 GLU cc_start: 0.8143 (tp30) cc_final: 0.7681 (mm-30) REVERT: I 92 GLN cc_start: 0.8733 (tt0) cc_final: 0.8434 (tt0) REVERT: I 98 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: J 4 GLN cc_start: 0.8414 (tp40) cc_final: 0.7985 (mm-40) REVERT: J 28 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7289 (mmp-170) REVERT: J 52 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7675 (mt-10) REVERT: J 71 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8671 (mtpp) REVERT: J 109 SER cc_start: 0.8830 (t) cc_final: 0.8547 (m) REVERT: J 123 GLU cc_start: 0.7481 (mp0) cc_final: 0.7276 (mp0) REVERT: J 126 MET cc_start: 0.7800 (mtp) cc_final: 0.7373 (mtp) REVERT: K 60 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7313 (mtm180) REVERT: K 77 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8487 (tm-30) REVERT: K 98 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: K 111 ASP cc_start: 0.8439 (p0) cc_final: 0.8101 (p0) REVERT: L 20 GLN cc_start: 0.7601 (tt0) cc_final: 0.7036 (tt0) REVERT: L 23 THR cc_start: 0.8574 (m) cc_final: 0.8171 (p) REVERT: L 71 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8104 (mtmm) REVERT: L 76 ASP cc_start: 0.8130 (t0) cc_final: 0.7908 (t0) REVERT: L 98 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: L 134 PHE cc_start: 0.8263 (t80) cc_final: 0.8019 (t80) REVERT: M 7 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8088 (mtpp) REVERT: M 12 LYS cc_start: 0.8640 (mttp) cc_final: 0.8270 (mtpp) REVERT: M 70 PHE cc_start: 0.9293 (t80) cc_final: 0.8773 (t80) REVERT: M 76 ASP cc_start: 0.8322 (t0) cc_final: 0.7995 (t0) REVERT: M 90 GLU cc_start: 0.8061 (tp30) cc_final: 0.7742 (mm-30) REVERT: M 98 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: M 111 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7936 (p0) REVERT: M 123 GLU cc_start: 0.7054 (mp0) cc_final: 0.6490 (mp0) REVERT: M 126 MET cc_start: 0.7934 (mtp) cc_final: 0.6783 (mtp) REVERT: N 4 GLN cc_start: 0.8481 (tp40) cc_final: 0.7966 (mm-40) REVERT: N 12 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7753 (mmmm) REVERT: N 14 ASP cc_start: 0.7633 (m-30) cc_final: 0.6935 (m-30) REVERT: N 28 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7320 (mmp-170) REVERT: N 78 ARG cc_start: 0.8916 (tpt170) cc_final: 0.8470 (tpt90) REVERT: N 85 ASP cc_start: 0.8028 (p0) cc_final: 0.7764 (p0) REVERT: O 12 LYS cc_start: 0.8748 (mttp) cc_final: 0.8319 (mtpp) REVERT: O 60 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7429 (mtm180) REVERT: O 98 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: P 23 THR cc_start: 0.8929 (m) cc_final: 0.8651 (p) REVERT: Q 52 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7647 (mt-10) REVERT: Q 98 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: Q 126 MET cc_start: 0.7498 (mtp) cc_final: 0.7103 (mtp) REVERT: R 4 GLN cc_start: 0.8499 (tp40) cc_final: 0.8182 (tp40) REVERT: R 28 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7255 (mmp-170) REVERT: R 71 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8519 (mtmm) REVERT: R 90 GLU cc_start: 0.8492 (tp30) cc_final: 0.8148 (tp30) REVERT: R 123 GLU cc_start: 0.7498 (mp0) cc_final: 0.7275 (mp0) REVERT: S 60 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7353 (mtm180) REVERT: S 69 VAL cc_start: 0.9604 (m) cc_final: 0.9291 (p) REVERT: S 98 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7982 (m-10) REVERT: T 4 GLN cc_start: 0.8673 (tp40) cc_final: 0.8454 (mm-40) REVERT: T 22 GLU cc_start: 0.7080 (mp0) cc_final: 0.6605 (mp0) REVERT: T 23 THR cc_start: 0.8714 (m) cc_final: 0.8325 (p) REVERT: T 44 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (tp) REVERT: T 47 GLN cc_start: 0.7977 (mp10) cc_final: 0.7624 (pm20) REVERT: T 50 TRP cc_start: 0.8323 (m100) cc_final: 0.8036 (m100) REVERT: U 14 ASP cc_start: 0.7360 (m-30) cc_final: 0.7124 (m-30) REVERT: U 35 ASN cc_start: 0.8510 (m-40) cc_final: 0.8245 (m-40) REVERT: U 76 ASP cc_start: 0.8665 (t0) cc_final: 0.8147 (t0) REVERT: U 90 GLU cc_start: 0.8143 (tp30) cc_final: 0.7685 (mm-30) REVERT: U 92 GLN cc_start: 0.8743 (tt0) cc_final: 0.8446 (tt0) REVERT: U 98 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7685 (m-80) REVERT: V 4 GLN cc_start: 0.8412 (tp40) cc_final: 0.7979 (mm-40) REVERT: V 28 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7288 (mmp-170) REVERT: V 52 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7742 (mt-10) REVERT: V 71 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8672 (mtpp) REVERT: V 109 SER cc_start: 0.8825 (t) cc_final: 0.8547 (m) REVERT: V 126 MET cc_start: 0.7800 (mtp) cc_final: 0.7363 (mtp) REVERT: W 60 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7301 (mtm180) REVERT: W 77 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8491 (tm-30) REVERT: W 98 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8146 (m-10) REVERT: W 111 ASP cc_start: 0.8428 (p0) cc_final: 0.8096 (p0) REVERT: X 20 GLN cc_start: 0.7597 (tt0) cc_final: 0.7037 (tt0) REVERT: X 23 THR cc_start: 0.8582 (m) cc_final: 0.8170 (p) REVERT: X 50 TRP cc_start: 0.8990 (m100) cc_final: 0.8498 (m100) REVERT: X 71 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8097 (mtmm) REVERT: X 76 ASP cc_start: 0.8128 (t0) cc_final: 0.7905 (t0) outliers start: 120 outliers final: 41 residues processed: 1001 average time/residue: 0.3550 time to fit residues: 541.4950 Evaluate side-chains 863 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 803 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 283 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 47 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN J 47 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 GLN K 92 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN ** Q 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 GLN ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN ** U 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 GLN W 92 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24216 Z= 0.200 Angle : 0.682 7.694 32712 Z= 0.352 Chirality : 0.051 0.327 3648 Planarity : 0.004 0.043 4368 Dihedral : 5.690 26.730 3384 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.28 % Allowed : 19.76 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.13), residues: 3168 helix: -2.98 (0.15), residues: 480 sheet: -0.86 (0.14), residues: 1176 loop : -2.57 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 50 HIS 0.007 0.001 HIS D 116 PHE 0.020 0.002 PHE B 91 TYR 0.020 0.002 TYR B 122 ARG 0.005 0.001 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 884 time to evaluate : 2.308 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: B 7 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8073 (mtpp) REVERT: B 12 LYS cc_start: 0.8578 (mttp) cc_final: 0.8283 (mtpp) REVERT: B 35 ASN cc_start: 0.8654 (m-40) cc_final: 0.8006 (m110) REVERT: B 47 GLN cc_start: 0.8538 (pm20) cc_final: 0.8319 (pm20) REVERT: B 70 PHE cc_start: 0.9316 (t80) cc_final: 0.8674 (t80) REVERT: B 76 ASP cc_start: 0.8400 (t0) cc_final: 0.7903 (t0) REVERT: B 98 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: B 111 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 123 GLU cc_start: 0.7290 (mp0) cc_final: 0.6505 (mp0) REVERT: A 28 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7387 (mmp-170) REVERT: A 85 ASP cc_start: 0.7931 (p0) cc_final: 0.7498 (p0) REVERT: C 12 LYS cc_start: 0.8799 (mttp) cc_final: 0.8409 (mtpp) REVERT: C 60 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7273 (mtm180) REVERT: C 98 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8077 (m-10) REVERT: D 21 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7360 (m-10) REVERT: D 22 GLU cc_start: 0.7033 (mp0) cc_final: 0.6610 (mp0) REVERT: D 76 ASP cc_start: 0.7858 (t0) cc_final: 0.7642 (t0) REVERT: E 37 GLU cc_start: 0.8156 (tp30) cc_final: 0.7820 (mm-30) REVERT: E 90 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: E 98 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: F 4 GLN cc_start: 0.8564 (tp40) cc_final: 0.8182 (mm-40) REVERT: F 28 ARG cc_start: 0.8145 (mtm180) cc_final: 0.7288 (mmp-170) REVERT: F 98 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: G 60 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7351 (mtm180) REVERT: G 92 GLN cc_start: 0.8654 (tt0) cc_final: 0.8399 (tt0) REVERT: G 98 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: H 4 GLN cc_start: 0.8688 (tp40) cc_final: 0.8434 (mm-40) REVERT: H 23 THR cc_start: 0.8573 (m) cc_final: 0.8116 (p) REVERT: H 50 TRP cc_start: 0.8292 (m100) cc_final: 0.7978 (m100) REVERT: H 71 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8480 (mtmm) REVERT: H 98 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: I 76 ASP cc_start: 0.8741 (t0) cc_final: 0.8232 (t0) REVERT: I 90 GLU cc_start: 0.8146 (tp30) cc_final: 0.7777 (mm-30) REVERT: I 98 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: J 4 GLN cc_start: 0.8436 (tp40) cc_final: 0.7916 (mm-40) REVERT: J 28 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7301 (mmp-170) REVERT: J 52 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7690 (mt-10) REVERT: J 90 GLU cc_start: 0.8528 (tp30) cc_final: 0.8291 (mm-30) REVERT: J 109 SER cc_start: 0.8801 (t) cc_final: 0.8422 (m) REVERT: K 77 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8475 (tm-30) REVERT: K 98 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: L 23 THR cc_start: 0.8387 (m) cc_final: 0.7834 (p) REVERT: L 45 GLU cc_start: 0.7582 (pp20) cc_final: 0.7293 (pp20) REVERT: L 47 GLN cc_start: 0.8247 (mp10) cc_final: 0.7916 (mp10) REVERT: L 71 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8225 (mttp) REVERT: L 98 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: L 134 PHE cc_start: 0.8309 (t80) cc_final: 0.8015 (t80) REVERT: M 7 LYS cc_start: 0.8305 (mtmm) cc_final: 0.8063 (mtpp) REVERT: M 12 LYS cc_start: 0.8580 (mttp) cc_final: 0.8283 (mtpp) REVERT: M 35 ASN cc_start: 0.8664 (m-40) cc_final: 0.8004 (m110) REVERT: M 47 GLN cc_start: 0.8548 (pm20) cc_final: 0.8332 (pm20) REVERT: M 70 PHE cc_start: 0.9318 (t80) cc_final: 0.8782 (t80) REVERT: M 76 ASP cc_start: 0.8408 (t0) cc_final: 0.7959 (t0) REVERT: M 98 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: M 111 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7980 (p0) REVERT: M 123 GLU cc_start: 0.7301 (mp0) cc_final: 0.6507 (mp0) REVERT: N 28 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7381 (mmp-170) REVERT: N 85 ASP cc_start: 0.7923 (p0) cc_final: 0.7496 (p0) REVERT: O 12 LYS cc_start: 0.8790 (mttp) cc_final: 0.8404 (mtpp) REVERT: O 60 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7284 (mtm180) REVERT: O 98 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8080 (m-10) REVERT: P 20 GLN cc_start: 0.7314 (tt0) cc_final: 0.6989 (tt0) REVERT: P 76 ASP cc_start: 0.7800 (t0) cc_final: 0.7382 (t0) REVERT: Q 37 GLU cc_start: 0.8157 (tp30) cc_final: 0.7832 (mm-30) REVERT: Q 90 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: Q 98 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: R 4 GLN cc_start: 0.8558 (tp40) cc_final: 0.8186 (mm-40) REVERT: R 28 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7251 (mmp-170) REVERT: R 98 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: S 60 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7358 (mtm180) REVERT: S 69 VAL cc_start: 0.9601 (m) cc_final: 0.9300 (p) REVERT: S 92 GLN cc_start: 0.8657 (tt0) cc_final: 0.8405 (tt0) REVERT: S 98 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: T 4 GLN cc_start: 0.8684 (tp40) cc_final: 0.8430 (mm-40) REVERT: T 23 THR cc_start: 0.8566 (m) cc_final: 0.8114 (p) REVERT: T 50 TRP cc_start: 0.8325 (m100) cc_final: 0.8013 (m100) REVERT: T 71 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8475 (mtmm) REVERT: T 98 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7787 (m-10) REVERT: U 76 ASP cc_start: 0.8748 (t0) cc_final: 0.8238 (t0) REVERT: U 90 GLU cc_start: 0.8144 (tp30) cc_final: 0.7776 (mm-30) REVERT: U 98 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: V 4 GLN cc_start: 0.8435 (tp40) cc_final: 0.7912 (mm-40) REVERT: V 28 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7298 (mmp-170) REVERT: V 52 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7785 (mt-10) REVERT: V 90 GLU cc_start: 0.8531 (tp30) cc_final: 0.8287 (mm-30) REVERT: V 109 SER cc_start: 0.8794 (t) cc_final: 0.8418 (m) REVERT: W 77 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8477 (tm-30) REVERT: W 98 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8141 (m-10) REVERT: W 134 PHE cc_start: 0.8070 (t80) cc_final: 0.7857 (t80) REVERT: X 23 THR cc_start: 0.8383 (m) cc_final: 0.7830 (p) REVERT: X 45 GLU cc_start: 0.7540 (pp20) cc_final: 0.7275 (pp20) REVERT: X 47 GLN cc_start: 0.8213 (mp10) cc_final: 0.7897 (mp10) REVERT: X 71 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8232 (mttp) REVERT: X 134 PHE cc_start: 0.8156 (t80) cc_final: 0.7949 (t80) outliers start: 128 outliers final: 58 residues processed: 926 average time/residue: 0.3483 time to fit residues: 493.2517 Evaluate side-chains 881 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 801 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 126 MET Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 123 GLU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 10.0000 chunk 213 optimal weight: 0.0970 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN D 102 GLN E 47 GLN F 20 GLN G 116 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN I 47 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 HIS ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 HIS ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 20 GLN S 116 HIS ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 GLN U 47 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24216 Z= 0.326 Angle : 0.715 8.062 32712 Z= 0.368 Chirality : 0.052 0.303 3648 Planarity : 0.004 0.025 4368 Dihedral : 5.803 28.358 3384 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.19 % Allowed : 21.70 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.13), residues: 3168 helix: -2.13 (0.19), residues: 480 sheet: -0.78 (0.14), residues: 1152 loop : -2.81 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 50 HIS 0.004 0.001 HIS D 116 PHE 0.021 0.002 PHE Q 91 TYR 0.019 0.002 TYR V 122 ARG 0.005 0.001 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 824 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8839 (mttp) cc_final: 0.8352 (mtpp) REVERT: B 31 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8051 (ttm-80) REVERT: B 35 ASN cc_start: 0.8691 (m-40) cc_final: 0.8110 (m110) REVERT: B 47 GLN cc_start: 0.8571 (pm20) cc_final: 0.8301 (pm20) REVERT: B 76 ASP cc_start: 0.8488 (t0) cc_final: 0.7865 (t0) REVERT: B 98 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: B 111 ASP cc_start: 0.8587 (p0) cc_final: 0.7794 (p0) REVERT: A 4 GLN cc_start: 0.8236 (tp40) cc_final: 0.7897 (mm-40) REVERT: A 12 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8116 (mmmm) REVERT: A 28 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7241 (mmp-170) REVERT: A 85 ASP cc_start: 0.7884 (p0) cc_final: 0.7444 (p0) REVERT: C 60 ARG cc_start: 0.7719 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: C 98 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: D 8 ASP cc_start: 0.7878 (m-30) cc_final: 0.7615 (m-30) REVERT: D 21 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7247 (m-10) REVERT: D 76 ASP cc_start: 0.8044 (t0) cc_final: 0.7679 (t0) REVERT: D 98 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: E 37 GLU cc_start: 0.8199 (tp30) cc_final: 0.7820 (mm-30) REVERT: E 76 ASP cc_start: 0.8628 (t0) cc_final: 0.8420 (t0) REVERT: E 90 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: E 98 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: F 28 ARG cc_start: 0.8481 (mtm180) cc_final: 0.7299 (mmp-170) REVERT: F 117 ASN cc_start: 0.9283 (p0) cc_final: 0.9066 (p0) REVERT: G 98 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: H 23 THR cc_start: 0.8693 (m) cc_final: 0.8322 (p) REVERT: H 44 LEU cc_start: 0.8896 (tm) cc_final: 0.8672 (tp) REVERT: H 50 TRP cc_start: 0.8271 (m100) cc_final: 0.7787 (m100) REVERT: H 76 ASP cc_start: 0.8055 (t0) cc_final: 0.7822 (t0) REVERT: H 98 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7541 (m-10) REVERT: I 35 ASN cc_start: 0.8649 (m110) cc_final: 0.8095 (m-40) REVERT: I 76 ASP cc_start: 0.8888 (t0) cc_final: 0.8200 (t0) REVERT: I 78 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8522 (tpt-90) REVERT: I 90 GLU cc_start: 0.8039 (tp30) cc_final: 0.7647 (mm-30) REVERT: I 98 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: I 111 ASP cc_start: 0.8044 (p0) cc_final: 0.7839 (p0) REVERT: J 28 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7344 (mmp-170) REVERT: J 52 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8147 (mt-10) REVERT: K 92 GLN cc_start: 0.8705 (tt0) cc_final: 0.8278 (tt0) REVERT: K 98 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: L 8 ASP cc_start: 0.7937 (m-30) cc_final: 0.7617 (m-30) REVERT: L 23 THR cc_start: 0.8295 (m) cc_final: 0.7816 (p) REVERT: L 28 ARG cc_start: 0.8757 (mtm180) cc_final: 0.8481 (mtm180) REVERT: L 45 GLU cc_start: 0.7765 (pp20) cc_final: 0.7323 (pp20) REVERT: L 71 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8347 (mttp) REVERT: L 98 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: L 134 PHE cc_start: 0.8441 (t80) cc_final: 0.8117 (t80) REVERT: M 12 LYS cc_start: 0.8838 (mttp) cc_final: 0.8343 (mtpp) REVERT: M 31 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: M 35 ASN cc_start: 0.8693 (m-40) cc_final: 0.8100 (m110) REVERT: M 47 GLN cc_start: 0.8585 (pm20) cc_final: 0.8317 (pm20) REVERT: M 76 ASP cc_start: 0.8505 (t0) cc_final: 0.7868 (t0) REVERT: M 98 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: M 111 ASP cc_start: 0.8613 (p0) cc_final: 0.7806 (p0) REVERT: N 4 GLN cc_start: 0.8240 (tp40) cc_final: 0.7896 (mm-40) REVERT: N 12 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8119 (mmmm) REVERT: N 28 ARG cc_start: 0.8332 (mtm180) cc_final: 0.7304 (mmp-170) REVERT: N 85 ASP cc_start: 0.7890 (p0) cc_final: 0.7464 (p0) REVERT: O 60 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7454 (mtm-85) REVERT: O 98 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: P 8 ASP cc_start: 0.7939 (m-30) cc_final: 0.7671 (m-30) REVERT: P 76 ASP cc_start: 0.8044 (t0) cc_final: 0.7624 (t0) REVERT: P 98 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: Q 37 GLU cc_start: 0.8201 (tp30) cc_final: 0.7829 (mm-30) REVERT: Q 76 ASP cc_start: 0.8631 (t0) cc_final: 0.8423 (t0) REVERT: Q 90 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: Q 98 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: R 28 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7266 (mmp-170) REVERT: R 117 ASN cc_start: 0.9283 (p0) cc_final: 0.9067 (p0) REVERT: S 98 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: T 23 THR cc_start: 0.8693 (m) cc_final: 0.8320 (p) REVERT: T 44 LEU cc_start: 0.8896 (tm) cc_final: 0.8671 (tp) REVERT: T 50 TRP cc_start: 0.8282 (m100) cc_final: 0.7790 (m100) REVERT: T 76 ASP cc_start: 0.8032 (t0) cc_final: 0.7750 (t0) REVERT: T 98 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: U 35 ASN cc_start: 0.8628 (m110) cc_final: 0.8081 (m-40) REVERT: U 76 ASP cc_start: 0.8894 (t0) cc_final: 0.8202 (t0) REVERT: U 78 ARG cc_start: 0.8741 (tpt90) cc_final: 0.8528 (tpt-90) REVERT: U 90 GLU cc_start: 0.8033 (tp30) cc_final: 0.7657 (mm-30) REVERT: U 98 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: U 111 ASP cc_start: 0.8031 (p0) cc_final: 0.7829 (p0) REVERT: V 28 ARG cc_start: 0.8310 (mtm180) cc_final: 0.7349 (mmp-170) REVERT: W 98 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: W 134 PHE cc_start: 0.8334 (t80) cc_final: 0.8079 (t80) REVERT: X 8 ASP cc_start: 0.7989 (m-30) cc_final: 0.7630 (m-30) REVERT: X 23 THR cc_start: 0.8282 (m) cc_final: 0.7806 (p) REVERT: X 28 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8487 (mtm180) REVERT: X 45 GLU cc_start: 0.7726 (pp20) cc_final: 0.7279 (pp20) REVERT: X 71 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8349 (mttp) REVERT: X 92 GLN cc_start: 0.8555 (tt0) cc_final: 0.8285 (tt0) REVERT: X 98 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7379 (m-80) outliers start: 150 outliers final: 82 residues processed: 879 average time/residue: 0.3537 time to fit residues: 484.3051 Evaluate side-chains 833 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 728 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 124 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 224 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 20 GLN F 102 GLN G 92 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN I 47 GLN ** I 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 20 GLN R 102 GLN S 92 GLN T 92 GLN U 47 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN W 116 HIS X 20 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 24216 Z= 0.510 Angle : 0.810 8.474 32712 Z= 0.422 Chirality : 0.054 0.350 3648 Planarity : 0.004 0.029 4368 Dihedral : 6.238 28.497 3384 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 7.67 % Allowed : 22.24 % Favored : 70.09 % 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: -3.03 (0.13), residues: 3168 helix: -1.78 (0.21), residues: 480 sheet: -1.13 (0.14), residues: 1200 loop : -2.84 (0.13), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 50 HIS 0.005 0.002 HIS X 116 PHE 0.027 0.002 PHE Q 91 TYR 0.018 0.002 TYR N 122 ARG 0.006 0.001 ARG M 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 771 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 LYS cc_start: 0.8954 (mttp) cc_final: 0.8398 (mtpp) REVERT: B 47 GLN cc_start: 0.8651 (pm20) cc_final: 0.8346 (pm20) REVERT: B 76 ASP cc_start: 0.8626 (t0) cc_final: 0.7985 (t0) REVERT: B 98 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.7322 (m-10) REVERT: A 4 GLN cc_start: 0.8320 (tp40) cc_final: 0.8112 (mm-40) REVERT: A 12 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8192 (mmmm) REVERT: A 28 ARG cc_start: 0.8688 (mtm180) cc_final: 0.7298 (mmp-170) REVERT: A 85 ASP cc_start: 0.7967 (p0) cc_final: 0.7472 (p0) REVERT: C 60 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7337 (mtm180) REVERT: C 98 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8196 (m-10) REVERT: C 110 ILE cc_start: 0.8948 (tp) cc_final: 0.8745 (tp) REVERT: D 8 ASP cc_start: 0.7976 (m-30) cc_final: 0.7723 (m-30) REVERT: D 21 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (m-10) REVERT: D 71 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8623 (mtmm) REVERT: D 76 ASP cc_start: 0.8184 (t0) cc_final: 0.7955 (t0) REVERT: D 98 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: E 76 ASP cc_start: 0.8993 (t0) cc_final: 0.8388 (t0) REVERT: E 90 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: E 98 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: F 4 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8332 (mm-40) REVERT: F 28 ARG cc_start: 0.8764 (mtm180) cc_final: 0.7204 (mmp-170) REVERT: F 98 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: G 8 ASP cc_start: 0.7863 (m-30) cc_final: 0.7633 (m-30) REVERT: G 98 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8671 (m-10) REVERT: H 23 THR cc_start: 0.8931 (m) cc_final: 0.8637 (p) REVERT: H 50 TRP cc_start: 0.8285 (m100) cc_final: 0.7639 (m100) REVERT: H 76 ASP cc_start: 0.8228 (t0) cc_final: 0.7827 (t0) REVERT: H 98 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: I 76 ASP cc_start: 0.8981 (t0) cc_final: 0.8269 (t0) REVERT: I 78 ARG cc_start: 0.8816 (tpt90) cc_final: 0.8534 (tpt-90) REVERT: I 98 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: J 27 LEU cc_start: 0.9495 (pt) cc_final: 0.9288 (pt) REVERT: J 28 ARG cc_start: 0.8671 (mtm180) cc_final: 0.7231 (mmp-170) REVERT: J 52 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7940 (mt-10) REVERT: J 76 ASP cc_start: 0.8445 (t0) cc_final: 0.8240 (t0) REVERT: K 77 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8542 (tp30) REVERT: K 92 GLN cc_start: 0.8922 (tt0) cc_final: 0.8453 (tt0) REVERT: K 98 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: L 8 ASP cc_start: 0.7956 (m-30) cc_final: 0.7601 (m-30) REVERT: L 23 THR cc_start: 0.8590 (m) cc_final: 0.8246 (p) REVERT: L 45 GLU cc_start: 0.7871 (pp20) cc_final: 0.7405 (pp20) REVERT: L 47 GLN cc_start: 0.8351 (mp10) cc_final: 0.7876 (mp10) REVERT: L 71 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8500 (mtmm) REVERT: L 76 ASP cc_start: 0.8219 (t0) cc_final: 0.8007 (t0) REVERT: L 92 GLN cc_start: 0.8599 (tt0) cc_final: 0.8161 (tt0) REVERT: L 98 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: M 12 LYS cc_start: 0.8955 (mttp) cc_final: 0.8395 (mtpp) REVERT: M 47 GLN cc_start: 0.8666 (pm20) cc_final: 0.8362 (pm20) REVERT: M 76 ASP cc_start: 0.8630 (t0) cc_final: 0.7997 (t0) REVERT: M 98 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: N 4 GLN cc_start: 0.8316 (tp40) cc_final: 0.8111 (mm-40) REVERT: N 12 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8288 (mmmm) REVERT: N 28 ARG cc_start: 0.8670 (mtm180) cc_final: 0.7278 (mmp-170) REVERT: N 85 ASP cc_start: 0.7953 (p0) cc_final: 0.7454 (p0) REVERT: O 98 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8152 (m-10) REVERT: O 110 ILE cc_start: 0.8973 (tp) cc_final: 0.8771 (tp) REVERT: P 8 ASP cc_start: 0.7985 (m-30) cc_final: 0.7718 (m-30) REVERT: P 15 LEU cc_start: 0.8378 (mm) cc_final: 0.7716 (mm) REVERT: P 20 GLN cc_start: 0.7530 (tt0) cc_final: 0.7026 (tt0) REVERT: P 22 GLU cc_start: 0.7488 (mp0) cc_final: 0.6776 (mp0) REVERT: P 76 ASP cc_start: 0.8172 (t0) cc_final: 0.7915 (t0) REVERT: P 98 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: Q 76 ASP cc_start: 0.8991 (t0) cc_final: 0.8393 (t0) REVERT: Q 90 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: Q 98 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: R 4 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8346 (mm-40) REVERT: R 28 ARG cc_start: 0.8767 (mtm180) cc_final: 0.7191 (mmp-170) REVERT: R 98 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: S 8 ASP cc_start: 0.7856 (m-30) cc_final: 0.7629 (m-30) REVERT: S 98 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8671 (m-10) REVERT: T 23 THR cc_start: 0.8937 (m) cc_final: 0.8648 (p) REVERT: T 50 TRP cc_start: 0.8293 (m100) cc_final: 0.7646 (m100) REVERT: T 76 ASP cc_start: 0.8211 (t0) cc_final: 0.7805 (t0) REVERT: T 98 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: U 76 ASP cc_start: 0.8984 (t0) cc_final: 0.8275 (t0) REVERT: U 78 ARG cc_start: 0.8812 (tpt90) cc_final: 0.8533 (tpt-90) REVERT: U 98 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: V 27 LEU cc_start: 0.9495 (pt) cc_final: 0.9287 (pt) REVERT: V 28 ARG cc_start: 0.8668 (mtm180) cc_final: 0.7235 (mmp-170) REVERT: V 76 ASP cc_start: 0.8445 (t0) cc_final: 0.8242 (t0) REVERT: W 77 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8515 (tp30) REVERT: W 98 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: W 134 PHE cc_start: 0.8594 (t80) cc_final: 0.8296 (t80) REVERT: X 8 ASP cc_start: 0.7988 (m-30) cc_final: 0.7637 (m-30) REVERT: X 20 GLN cc_start: 0.7530 (tt0) cc_final: 0.7292 (tt0) REVERT: X 45 GLU cc_start: 0.7874 (pp20) cc_final: 0.6913 (pp20) REVERT: X 47 GLN cc_start: 0.8326 (mp10) cc_final: 0.7461 (mp10) REVERT: X 71 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8511 (mtmm) REVERT: X 76 ASP cc_start: 0.8201 (t0) cc_final: 0.7985 (t0) REVERT: X 98 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7685 (m-80) outliers start: 186 outliers final: 104 residues processed: 853 average time/residue: 0.3270 time to fit residues: 440.2773 Evaluate side-chains 837 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 708 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain O residue 126 MET Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 44 LEU Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 87 GLU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 301 optimal weight: 7.9990 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 20 GLN F 102 GLN F 116 HIS F 117 ASN ** H 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN I 102 GLN J 47 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 20 GLN ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 HIS R 117 ASN S 102 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN U 102 GLN V 47 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 GLN ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24216 Z= 0.249 Angle : 0.736 10.746 32712 Z= 0.367 Chirality : 0.052 0.281 3648 Planarity : 0.003 0.025 4368 Dihedral : 5.776 27.725 3384 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 6.15 % Allowed : 25.37 % Favored : 68.48 % 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: -2.83 (0.13), residues: 3168 helix: -1.42 (0.22), residues: 480 sheet: -0.97 (0.14), residues: 1152 loop : -2.80 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 50 HIS 0.005 0.002 HIS P 116 PHE 0.022 0.002 PHE D 21 TYR 0.022 0.001 TYR J 122 ARG 0.004 0.001 ARG I 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 831 time to evaluate : 2.776 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: B 12 LYS cc_start: 0.8871 (mttp) cc_final: 0.8514 (mtpp) REVERT: B 33 SER cc_start: 0.9220 (t) cc_final: 0.8499 (p) REVERT: B 35 ASN cc_start: 0.8670 (m-40) cc_final: 0.8127 (m110) REVERT: B 47 GLN cc_start: 0.8611 (pm20) cc_final: 0.8326 (pm20) REVERT: B 76 ASP cc_start: 0.8452 (t0) cc_final: 0.7841 (t0) REVERT: B 92 GLN cc_start: 0.9005 (tt0) cc_final: 0.8445 (tt0) REVERT: B 98 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 111 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (p0) REVERT: B 123 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 4 GLN cc_start: 0.8267 (tp40) cc_final: 0.8043 (mm-40) REVERT: A 12 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8295 (mtpp) REVERT: A 28 ARG cc_start: 0.8505 (mtm180) cc_final: 0.6969 (mmp-170) REVERT: A 76 ASP cc_start: 0.8123 (t0) cc_final: 0.7865 (t0) REVERT: A 85 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7276 (p0) REVERT: C 98 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: D 8 ASP cc_start: 0.7882 (m-30) cc_final: 0.7647 (m-30) REVERT: D 21 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7443 (m-10) REVERT: D 22 GLU cc_start: 0.7105 (mp0) cc_final: 0.6830 (mp0) REVERT: D 71 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8527 (mtmm) REVERT: D 76 ASP cc_start: 0.8182 (t0) cc_final: 0.7855 (t0) REVERT: D 98 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: E 76 ASP cc_start: 0.8874 (t0) cc_final: 0.8469 (t0) REVERT: E 90 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: E 98 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7205 (m-80) REVERT: E 126 MET cc_start: 0.7707 (mtp) cc_final: 0.7482 (mtp) REVERT: E 134 PHE cc_start: 0.8779 (t80) cc_final: 0.8379 (t80) REVERT: F 4 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8403 (mm-40) REVERT: F 28 ARG cc_start: 0.8643 (mtm180) cc_final: 0.7141 (mmp-170) REVERT: F 98 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: G 76 ASP cc_start: 0.8353 (t0) cc_final: 0.8147 (t0) REVERT: G 98 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8402 (m-10) REVERT: H 22 GLU cc_start: 0.7191 (mp0) cc_final: 0.6896 (mp0) REVERT: H 45 GLU cc_start: 0.7763 (pm20) cc_final: 0.7405 (pp20) REVERT: H 50 TRP cc_start: 0.8211 (m100) cc_final: 0.7466 (m100) REVERT: H 76 ASP cc_start: 0.8102 (t0) cc_final: 0.7762 (t0) REVERT: H 98 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: I 35 ASN cc_start: 0.8609 (m110) cc_final: 0.7950 (m-40) REVERT: I 76 ASP cc_start: 0.8815 (t0) cc_final: 0.8314 (t0) REVERT: I 78 ARG cc_start: 0.8680 (tpt90) cc_final: 0.8316 (tpt-90) REVERT: I 92 GLN cc_start: 0.9144 (tt0) cc_final: 0.8654 (tt0) REVERT: I 98 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: I 111 ASP cc_start: 0.8511 (p0) cc_final: 0.8131 (p0) REVERT: J 4 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8226 (mm-40) REVERT: J 28 ARG cc_start: 0.8587 (mtm180) cc_final: 0.7052 (mmt180) REVERT: J 76 ASP cc_start: 0.8297 (t0) cc_final: 0.8020 (t0) REVERT: J 98 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: K 92 GLN cc_start: 0.8811 (tt0) cc_final: 0.8396 (tt0) REVERT: K 98 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7944 (m-10) REVERT: K 134 PHE cc_start: 0.8248 (t80) cc_final: 0.8013 (t80) REVERT: L 8 ASP cc_start: 0.7903 (m-30) cc_final: 0.7493 (m-30) REVERT: L 23 THR cc_start: 0.8341 (m) cc_final: 0.7915 (p) REVERT: L 28 ARG cc_start: 0.8833 (mtm180) cc_final: 0.8623 (mtm180) REVERT: L 47 GLN cc_start: 0.8375 (mp10) cc_final: 0.8126 (mp10) REVERT: L 98 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: M 12 LYS cc_start: 0.8866 (mttp) cc_final: 0.8506 (mtpp) REVERT: M 33 SER cc_start: 0.9226 (t) cc_final: 0.8524 (p) REVERT: M 35 ASN cc_start: 0.8672 (m-40) cc_final: 0.8120 (m110) REVERT: M 47 GLN cc_start: 0.8625 (pm20) cc_final: 0.8335 (pm20) REVERT: M 76 ASP cc_start: 0.8464 (t0) cc_final: 0.7839 (t0) REVERT: M 92 GLN cc_start: 0.9008 (tt0) cc_final: 0.8443 (tt0) REVERT: M 98 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: N 4 GLN cc_start: 0.8252 (tp40) cc_final: 0.8036 (mm-40) REVERT: N 12 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: N 28 ARG cc_start: 0.8491 (mtm180) cc_final: 0.7004 (mmp-170) REVERT: N 76 ASP cc_start: 0.8148 (t0) cc_final: 0.7912 (t0) REVERT: N 85 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7331 (p0) REVERT: N 123 GLU cc_start: 0.7591 (mp0) cc_final: 0.7338 (mp0) REVERT: O 80 ARG cc_start: 0.8899 (tmm160) cc_final: 0.8686 (tmm160) REVERT: O 98 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7973 (m-10) REVERT: P 8 ASP cc_start: 0.7880 (m-30) cc_final: 0.7636 (m-30) REVERT: P 98 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: Q 76 ASP cc_start: 0.8872 (t0) cc_final: 0.8470 (t0) REVERT: Q 90 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: Q 98 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: Q 126 MET cc_start: 0.7700 (mtp) cc_final: 0.7496 (mtp) REVERT: Q 134 PHE cc_start: 0.8784 (t80) cc_final: 0.8387 (t80) REVERT: R 4 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8412 (mm-40) REVERT: R 28 ARG cc_start: 0.8670 (mtm180) cc_final: 0.7172 (mmp-170) REVERT: R 98 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: S 98 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8445 (m-10) REVERT: T 23 THR cc_start: 0.8785 (m) cc_final: 0.8428 (p) REVERT: T 45 GLU cc_start: 0.7762 (pm20) cc_final: 0.7398 (pp20) REVERT: T 50 TRP cc_start: 0.8181 (m100) cc_final: 0.7465 (m100) REVERT: T 76 ASP cc_start: 0.8068 (t0) cc_final: 0.7716 (t0) REVERT: T 98 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: U 35 ASN cc_start: 0.8584 (m110) cc_final: 0.7979 (m-40) REVERT: U 76 ASP cc_start: 0.8820 (t0) cc_final: 0.8313 (t0) REVERT: U 78 ARG cc_start: 0.8678 (tpt90) cc_final: 0.8319 (tpt-90) REVERT: U 92 GLN cc_start: 0.9138 (tt0) cc_final: 0.8656 (tt0) REVERT: U 98 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: U 111 ASP cc_start: 0.8494 (p0) cc_final: 0.8115 (p0) REVERT: V 4 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8195 (mm-40) REVERT: V 28 ARG cc_start: 0.8587 (mtm180) cc_final: 0.7054 (mmt180) REVERT: V 76 ASP cc_start: 0.8301 (t0) cc_final: 0.8029 (t0) REVERT: V 98 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: V 100 ILE cc_start: 0.8892 (mm) cc_final: 0.8559 (mm) REVERT: W 98 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8054 (m-10) REVERT: W 134 PHE cc_start: 0.8485 (t80) cc_final: 0.8250 (t80) REVERT: X 8 ASP cc_start: 0.7893 (m-30) cc_final: 0.7505 (m-30) REVERT: X 23 THR cc_start: 0.8282 (m) cc_final: 0.7806 (p) REVERT: X 28 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8626 (mtm180) REVERT: X 45 GLU cc_start: 0.7865 (pp20) cc_final: 0.7438 (pp20) REVERT: X 47 GLN cc_start: 0.8354 (mp10) cc_final: 0.7838 (mp10) REVERT: X 98 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7367 (m-80) outliers start: 149 outliers final: 90 residues processed: 886 average time/residue: 0.3299 time to fit residues: 459.1947 Evaluate side-chains 865 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 745 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 32 ILE Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 20 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 92 GLN F 117 ASN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN I 92 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 92 GLN R 102 GLN R 117 ASN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN U 92 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24216 Z= 0.222 Angle : 0.734 10.471 32712 Z= 0.363 Chirality : 0.051 0.242 3648 Planarity : 0.003 0.026 4368 Dihedral : 5.513 23.930 3384 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 6.77 % Allowed : 27.02 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3168 helix: -1.22 (0.23), residues: 480 sheet: -0.99 (0.14), residues: 1176 loop : -2.85 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 50 HIS 0.004 0.001 HIS D 116 PHE 0.020 0.002 PHE D 21 TYR 0.023 0.001 TYR N 122 ARG 0.004 0.000 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 791 time to evaluate : 2.668 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: B 31 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8187 (ttm-80) REVERT: B 33 SER cc_start: 0.9244 (t) cc_final: 0.8582 (p) REVERT: B 35 ASN cc_start: 0.8631 (m-40) cc_final: 0.8051 (m110) REVERT: B 47 GLN cc_start: 0.8616 (pm20) cc_final: 0.8348 (pm20) REVERT: B 76 ASP cc_start: 0.8360 (t0) cc_final: 0.7881 (t0) REVERT: B 77 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 92 GLN cc_start: 0.8958 (tt0) cc_final: 0.8405 (tt0) REVERT: B 98 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: B 111 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8043 (p0) REVERT: B 123 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 12 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8343 (mtpp) REVERT: A 14 ASP cc_start: 0.7041 (m-30) cc_final: 0.6793 (m-30) REVERT: A 28 ARG cc_start: 0.8487 (mtm180) cc_final: 0.6954 (mmp-170) REVERT: A 76 ASP cc_start: 0.8164 (t0) cc_final: 0.7836 (t0) REVERT: A 85 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7165 (p0) REVERT: C 87 GLU cc_start: 0.8207 (pt0) cc_final: 0.7896 (pt0) REVERT: C 98 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: C 110 ILE cc_start: 0.8930 (tp) cc_final: 0.8665 (tp) REVERT: D 8 ASP cc_start: 0.7862 (m-30) cc_final: 0.7599 (m-30) REVERT: D 71 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8520 (mtmm) REVERT: D 76 ASP cc_start: 0.8167 (t0) cc_final: 0.7861 (t0) REVERT: D 98 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: E 76 ASP cc_start: 0.8851 (t0) cc_final: 0.8479 (t0) REVERT: E 90 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: E 98 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: E 126 MET cc_start: 0.7465 (mtp) cc_final: 0.7144 (mtp) REVERT: E 134 PHE cc_start: 0.8762 (t80) cc_final: 0.8325 (t80) REVERT: F 4 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8168 (mm-40) REVERT: F 28 ARG cc_start: 0.8622 (mtm180) cc_final: 0.7150 (mmp-170) REVERT: F 98 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7211 (m-80) REVERT: G 87 GLU cc_start: 0.7721 (pt0) cc_final: 0.7489 (pt0) REVERT: G 98 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8357 (m-10) REVERT: H 50 TRP cc_start: 0.7970 (m100) cc_final: 0.7549 (m100) REVERT: H 76 ASP cc_start: 0.8091 (t0) cc_final: 0.7739 (t0) REVERT: H 98 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: I 35 ASN cc_start: 0.8615 (m110) cc_final: 0.8065 (m-40) REVERT: I 76 ASP cc_start: 0.8768 (t0) cc_final: 0.8250 (t0) REVERT: I 92 GLN cc_start: 0.9010 (tt0) cc_final: 0.8591 (tt0) REVERT: I 98 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: I 111 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8021 (p0) REVERT: J 4 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8017 (mm-40) REVERT: J 27 LEU cc_start: 0.9346 (pt) cc_final: 0.9146 (pt) REVERT: J 28 ARG cc_start: 0.8549 (mtm180) cc_final: 0.7232 (mmp-170) REVERT: J 76 ASP cc_start: 0.8341 (t0) cc_final: 0.8019 (t0) REVERT: J 98 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: J 100 ILE cc_start: 0.8905 (mm) cc_final: 0.8575 (mm) REVERT: K 37 GLU cc_start: 0.7894 (tp30) cc_final: 0.7640 (tp30) REVERT: K 77 GLU cc_start: 0.9092 (tp30) cc_final: 0.8785 (tp30) REVERT: K 92 GLN cc_start: 0.8702 (tt0) cc_final: 0.8380 (tt0) REVERT: K 98 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.7943 (m-10) REVERT: L 7 LYS cc_start: 0.9231 (ptmm) cc_final: 0.8997 (ptmm) REVERT: L 23 THR cc_start: 0.8212 (m) cc_final: 0.7751 (p) REVERT: L 71 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8312 (mttm) REVERT: M 31 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8191 (ttm-80) REVERT: M 33 SER cc_start: 0.9246 (t) cc_final: 0.8603 (p) REVERT: M 35 ASN cc_start: 0.8634 (m-40) cc_final: 0.8059 (m110) REVERT: M 47 GLN cc_start: 0.8631 (pm20) cc_final: 0.8360 (pm20) REVERT: M 76 ASP cc_start: 0.8370 (t0) cc_final: 0.7878 (t0) REVERT: M 77 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8285 (tm-30) REVERT: M 92 GLN cc_start: 0.8961 (tt0) cc_final: 0.8407 (tt0) REVERT: M 98 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: M 111 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7801 (p0) REVERT: N 12 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: N 28 ARG cc_start: 0.8475 (mtm180) cc_final: 0.7084 (mmp-170) REVERT: N 76 ASP cc_start: 0.8205 (t0) cc_final: 0.7827 (t0) REVERT: N 85 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7190 (p0) REVERT: N 123 GLU cc_start: 0.7588 (mp0) cc_final: 0.7278 (mp0) REVERT: O 87 GLU cc_start: 0.8304 (pt0) cc_final: 0.7974 (pt0) REVERT: O 98 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: O 110 ILE cc_start: 0.8933 (tp) cc_final: 0.8674 (tp) REVERT: P 8 ASP cc_start: 0.7849 (m-30) cc_final: 0.7589 (m-30) REVERT: Q 76 ASP cc_start: 0.8849 (t0) cc_final: 0.8488 (t0) REVERT: Q 90 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: Q 98 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: Q 126 MET cc_start: 0.7448 (mtp) cc_final: 0.7163 (mtp) REVERT: Q 134 PHE cc_start: 0.8769 (t80) cc_final: 0.8334 (t80) REVERT: R 4 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8173 (mm-40) REVERT: R 28 ARG cc_start: 0.8642 (mtm180) cc_final: 0.7146 (mmp-170) REVERT: R 98 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7216 (m-80) REVERT: S 98 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: T 23 THR cc_start: 0.8655 (m) cc_final: 0.8254 (p) REVERT: T 50 TRP cc_start: 0.7963 (m100) cc_final: 0.7620 (m100) REVERT: T 76 ASP cc_start: 0.8065 (t0) cc_final: 0.7784 (t0) REVERT: T 98 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: U 35 ASN cc_start: 0.8590 (m110) cc_final: 0.8047 (m-40) REVERT: U 76 ASP cc_start: 0.8772 (t0) cc_final: 0.8250 (t0) REVERT: U 92 GLN cc_start: 0.9003 (tt0) cc_final: 0.8585 (tt0) REVERT: U 98 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7524 (m-80) REVERT: U 111 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8009 (p0) REVERT: V 4 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8228 (mm-40) REVERT: V 28 ARG cc_start: 0.8550 (mtm180) cc_final: 0.7235 (mmp-170) REVERT: V 76 ASP cc_start: 0.8341 (t0) cc_final: 0.8027 (t0) REVERT: V 98 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: V 100 ILE cc_start: 0.8860 (mm) cc_final: 0.8514 (mm) REVERT: W 37 GLU cc_start: 0.7906 (tp30) cc_final: 0.7637 (tp30) REVERT: W 98 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: W 134 PHE cc_start: 0.8407 (t80) cc_final: 0.8205 (t80) REVERT: X 7 LYS cc_start: 0.9249 (ptmm) cc_final: 0.8925 (ptmm) REVERT: X 8 ASP cc_start: 0.7800 (m-30) cc_final: 0.7431 (m-30) REVERT: X 23 THR cc_start: 0.8248 (m) cc_final: 0.7761 (p) REVERT: X 71 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8326 (mttm) REVERT: X 98 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7418 (m-80) outliers start: 164 outliers final: 96 residues processed: 859 average time/residue: 0.3273 time to fit residues: 443.2623 Evaluate side-chains 846 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 720 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 59 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN D 20 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 117 ASN G 92 GLN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 92 GLN O 92 GLN ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN Q 47 GLN R 117 ASN S 92 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 GLN ** X 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 GLN ** X 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24216 Z= 0.299 Angle : 0.764 11.148 32712 Z= 0.380 Chirality : 0.052 0.336 3648 Planarity : 0.004 0.025 4368 Dihedral : 5.637 23.637 3384 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.26 % Allowed : 28.14 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3168 helix: -1.08 (0.23), residues: 480 sheet: -1.00 (0.14), residues: 1176 loop : -2.85 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 50 HIS 0.007 0.001 HIS P 116 PHE 0.019 0.002 PHE C 21 TYR 0.015 0.001 TYR W 112 ARG 0.005 0.001 ARG W 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 727 time to evaluate : 2.828 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: B 33 SER cc_start: 0.9273 (t) cc_final: 0.8598 (p) REVERT: B 35 ASN cc_start: 0.8671 (m-40) cc_final: 0.8081 (m110) REVERT: B 47 GLN cc_start: 0.8610 (pm20) cc_final: 0.8338 (pm20) REVERT: B 76 ASP cc_start: 0.8465 (t0) cc_final: 0.7873 (t0) REVERT: B 78 ARG cc_start: 0.8707 (tpt90) cc_final: 0.8114 (tpt-90) REVERT: B 92 GLN cc_start: 0.9040 (tt0) cc_final: 0.8369 (tt0) REVERT: B 98 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: B 111 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7950 (p0) REVERT: A 12 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: A 28 ARG cc_start: 0.8551 (mtm180) cc_final: 0.7064 (mmp-170) REVERT: A 76 ASP cc_start: 0.8197 (t0) cc_final: 0.7849 (t0) REVERT: A 85 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7206 (p0) REVERT: A 98 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7623 (m-80) REVERT: C 77 GLU cc_start: 0.9162 (tp30) cc_final: 0.8858 (tp30) REVERT: C 98 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8189 (m-10) REVERT: C 110 ILE cc_start: 0.8905 (tp) cc_final: 0.8648 (tp) REVERT: D 8 ASP cc_start: 0.7878 (m-30) cc_final: 0.7625 (m-30) REVERT: D 71 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8553 (mtmm) REVERT: D 76 ASP cc_start: 0.8203 (t0) cc_final: 0.7861 (t0) REVERT: D 98 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: E 76 ASP cc_start: 0.8889 (t0) cc_final: 0.8492 (t0) REVERT: E 90 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: E 98 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: E 134 PHE cc_start: 0.8689 (t80) cc_final: 0.8292 (t80) REVERT: F 4 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8213 (mm-40) REVERT: F 28 ARG cc_start: 0.8694 (mtm180) cc_final: 0.7164 (mmp-170) REVERT: F 98 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: G 87 GLU cc_start: 0.7846 (pt0) cc_final: 0.7629 (pt0) REVERT: G 98 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: H 50 TRP cc_start: 0.7988 (m100) cc_final: 0.7683 (m100) REVERT: H 76 ASP cc_start: 0.8081 (t0) cc_final: 0.7659 (t0) REVERT: H 98 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: I 35 ASN cc_start: 0.8579 (m110) cc_final: 0.8005 (m-40) REVERT: I 76 ASP cc_start: 0.8829 (t0) cc_final: 0.8175 (t0) REVERT: I 78 ARG cc_start: 0.8600 (tpt90) cc_final: 0.8315 (tpt-90) REVERT: I 92 GLN cc_start: 0.8971 (tt0) cc_final: 0.8603 (tt0) REVERT: I 98 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: I 111 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8056 (p0) REVERT: J 4 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8037 (mm-40) REVERT: J 28 ARG cc_start: 0.8573 (mtm180) cc_final: 0.7184 (mmp-170) REVERT: J 76 ASP cc_start: 0.8367 (t0) cc_final: 0.8015 (t0) REVERT: J 98 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: J 100 ILE cc_start: 0.8942 (mm) cc_final: 0.8600 (mm) REVERT: K 37 GLU cc_start: 0.7920 (tp30) cc_final: 0.7623 (tp30) REVERT: K 77 GLU cc_start: 0.9235 (tp30) cc_final: 0.8881 (tp30) REVERT: K 92 GLN cc_start: 0.8785 (tt0) cc_final: 0.8424 (tt0) REVERT: K 98 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: L 7 LYS cc_start: 0.9310 (ptmm) cc_final: 0.9102 (ptmm) REVERT: M 33 SER cc_start: 0.9274 (t) cc_final: 0.8612 (p) REVERT: M 35 ASN cc_start: 0.8659 (m-40) cc_final: 0.8063 (m110) REVERT: M 47 GLN cc_start: 0.8626 (pm20) cc_final: 0.8359 (pm20) REVERT: M 76 ASP cc_start: 0.8468 (t0) cc_final: 0.7886 (t0) REVERT: M 78 ARG cc_start: 0.8711 (tpt90) cc_final: 0.8114 (tpt-90) REVERT: M 92 GLN cc_start: 0.9047 (tt0) cc_final: 0.8375 (tt0) REVERT: M 98 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: M 111 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7856 (p0) REVERT: N 12 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8352 (mtpp) REVERT: N 28 ARG cc_start: 0.8560 (mtm180) cc_final: 0.7105 (mmp-170) REVERT: N 76 ASP cc_start: 0.8192 (t0) cc_final: 0.7778 (t0) REVERT: N 85 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7259 (p0) REVERT: N 98 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: O 98 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: O 110 ILE cc_start: 0.8905 (tp) cc_final: 0.8652 (tp) REVERT: P 71 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8523 (mtmm) REVERT: Q 76 ASP cc_start: 0.8889 (t0) cc_final: 0.8487 (t0) REVERT: Q 90 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: Q 98 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: Q 134 PHE cc_start: 0.8695 (t80) cc_final: 0.8295 (t80) REVERT: R 4 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8214 (mm-40) REVERT: R 28 ARG cc_start: 0.8700 (mtm180) cc_final: 0.7144 (mmp-170) REVERT: R 98 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: S 98 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8238 (m-80) REVERT: T 23 THR cc_start: 0.8684 (m) cc_final: 0.8312 (p) REVERT: T 50 TRP cc_start: 0.7980 (m100) cc_final: 0.7675 (m100) REVERT: T 76 ASP cc_start: 0.8102 (t0) cc_final: 0.7810 (t0) REVERT: T 98 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: U 35 ASN cc_start: 0.8563 (m110) cc_final: 0.7997 (m-40) REVERT: U 76 ASP cc_start: 0.8831 (t0) cc_final: 0.8175 (t0) REVERT: U 78 ARG cc_start: 0.8597 (tpt90) cc_final: 0.8311 (tpt-90) REVERT: U 92 GLN cc_start: 0.8964 (tt0) cc_final: 0.8601 (tt0) REVERT: U 98 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: U 111 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8044 (p0) REVERT: V 4 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8047 (mm-40) REVERT: V 28 ARG cc_start: 0.8576 (mtm180) cc_final: 0.7174 (mmp-170) REVERT: V 76 ASP cc_start: 0.8363 (t0) cc_final: 0.8038 (t0) REVERT: V 98 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: V 100 ILE cc_start: 0.8908 (mm) cc_final: 0.8571 (mm) REVERT: W 37 GLU cc_start: 0.7886 (tp30) cc_final: 0.7597 (tp30) REVERT: W 77 GLU cc_start: 0.9195 (tp30) cc_final: 0.8786 (tp30) REVERT: W 98 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: W 134 PHE cc_start: 0.8490 (t80) cc_final: 0.8236 (t80) REVERT: X 8 ASP cc_start: 0.7875 (m-30) cc_final: 0.7436 (m-30) REVERT: X 98 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7291 (m-80) outliers start: 176 outliers final: 122 residues processed: 806 average time/residue: 0.3302 time to fit residues: 418.5844 Evaluate side-chains 857 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 703 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 90 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 90 GLU Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 37 GLU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 220 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 117 ASN G 92 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN Q 47 GLN R 117 ASN S 92 GLN ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24216 Z= 0.318 Angle : 0.789 14.136 32712 Z= 0.389 Chirality : 0.053 0.331 3648 Planarity : 0.004 0.030 4368 Dihedral : 5.740 23.724 3384 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 7.14 % Allowed : 27.81 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.13), residues: 3168 helix: -1.02 (0.23), residues: 480 sheet: -1.02 (0.14), residues: 1176 loop : -2.83 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 50 HIS 0.006 0.001 HIS P 116 PHE 0.018 0.002 PHE C 21 TYR 0.013 0.001 TYR W 112 ARG 0.005 0.001 ARG W 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 731 time to evaluate : 2.755 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: B 33 SER cc_start: 0.9282 (t) cc_final: 0.8639 (p) REVERT: B 35 ASN cc_start: 0.8691 (m-40) cc_final: 0.8096 (m110) REVERT: B 47 GLN cc_start: 0.8614 (pm20) cc_final: 0.8334 (pm20) REVERT: B 76 ASP cc_start: 0.8477 (t0) cc_final: 0.8187 (t0) REVERT: B 92 GLN cc_start: 0.9050 (tt0) cc_final: 0.8362 (tt0) REVERT: B 98 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.7267 (m-10) REVERT: B 111 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 12 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: A 28 ARG cc_start: 0.8575 (mtm180) cc_final: 0.7072 (mmp-170) REVERT: A 76 ASP cc_start: 0.8192 (t0) cc_final: 0.7826 (t0) REVERT: A 85 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7238 (p0) REVERT: A 98 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: C 77 GLU cc_start: 0.9171 (tp30) cc_final: 0.8872 (tp30) REVERT: C 98 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8172 (m-10) REVERT: C 110 ILE cc_start: 0.8924 (tp) cc_final: 0.8667 (tp) REVERT: D 8 ASP cc_start: 0.7893 (m-30) cc_final: 0.7667 (m-30) REVERT: D 22 GLU cc_start: 0.7072 (mp0) cc_final: 0.6418 (mp0) REVERT: D 71 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8562 (mtmm) REVERT: D 76 ASP cc_start: 0.8214 (t0) cc_final: 0.7892 (t0) REVERT: D 98 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: E 76 ASP cc_start: 0.8872 (t0) cc_final: 0.8467 (t0) REVERT: E 98 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: E 134 PHE cc_start: 0.8680 (t80) cc_final: 0.8281 (t80) REVERT: F 4 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8237 (mm-40) REVERT: F 28 ARG cc_start: 0.8694 (mtm180) cc_final: 0.7106 (mmp-170) REVERT: F 98 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: G 87 GLU cc_start: 0.7930 (pt0) cc_final: 0.7716 (pt0) REVERT: G 98 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: H 50 TRP cc_start: 0.8228 (m100) cc_final: 0.8000 (m100) REVERT: H 76 ASP cc_start: 0.8168 (t0) cc_final: 0.7719 (t0) REVERT: H 98 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: I 35 ASN cc_start: 0.8593 (m110) cc_final: 0.7982 (m-40) REVERT: I 76 ASP cc_start: 0.8852 (t0) cc_final: 0.8185 (t0) REVERT: I 78 ARG cc_start: 0.8550 (tpt90) cc_final: 0.8305 (tpt-90) REVERT: I 87 GLU cc_start: 0.8047 (pt0) cc_final: 0.7491 (pt0) REVERT: I 92 GLN cc_start: 0.8964 (tt0) cc_final: 0.8521 (tt0) REVERT: I 98 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: I 111 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8046 (p0) REVERT: I 123 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6579 (mt-10) REVERT: J 4 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8083 (mm-40) REVERT: J 28 ARG cc_start: 0.8576 (mtm180) cc_final: 0.7144 (mmp-170) REVERT: J 76 ASP cc_start: 0.8291 (t0) cc_final: 0.7954 (t0) REVERT: J 98 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: J 100 ILE cc_start: 0.8967 (mm) cc_final: 0.8617 (mm) REVERT: K 37 GLU cc_start: 0.7918 (tp30) cc_final: 0.7626 (tp30) REVERT: K 77 GLU cc_start: 0.9231 (tp30) cc_final: 0.8911 (tp30) REVERT: K 92 GLN cc_start: 0.8772 (tt0) cc_final: 0.8443 (tt0) REVERT: K 98 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.7979 (m-10) REVERT: L 28 ARG cc_start: 0.8803 (mtm180) cc_final: 0.8588 (mtm180) REVERT: M 33 SER cc_start: 0.9284 (t) cc_final: 0.8660 (p) REVERT: M 35 ASN cc_start: 0.8686 (m-40) cc_final: 0.8083 (m110) REVERT: M 47 GLN cc_start: 0.8633 (pm20) cc_final: 0.8355 (pm20) REVERT: M 76 ASP cc_start: 0.8486 (t0) cc_final: 0.8210 (t0) REVERT: M 92 GLN cc_start: 0.9044 (tt0) cc_final: 0.8382 (tt0) REVERT: M 98 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: N 12 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8398 (mtpp) REVERT: N 28 ARG cc_start: 0.8609 (mtm180) cc_final: 0.7115 (mmp-170) REVERT: N 76 ASP cc_start: 0.8197 (t0) cc_final: 0.7700 (t0) REVERT: N 85 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7303 (p0) REVERT: N 98 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: O 98 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8155 (m-10) REVERT: O 110 ILE cc_start: 0.8927 (tp) cc_final: 0.8671 (tp) REVERT: Q 76 ASP cc_start: 0.8874 (t0) cc_final: 0.8461 (t0) REVERT: Q 98 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: Q 134 PHE cc_start: 0.8686 (t80) cc_final: 0.8286 (t80) REVERT: R 4 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8244 (mm-40) REVERT: R 28 ARG cc_start: 0.8720 (mtm180) cc_final: 0.7134 (mmp-170) REVERT: R 98 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: S 98 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: T 23 THR cc_start: 0.8700 (m) cc_final: 0.8350 (p) REVERT: T 50 TRP cc_start: 0.8226 (m100) cc_final: 0.7969 (m100) REVERT: T 76 ASP cc_start: 0.8123 (t0) cc_final: 0.7811 (t0) REVERT: T 98 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: U 35 ASN cc_start: 0.8551 (m110) cc_final: 0.7983 (m-40) REVERT: U 76 ASP cc_start: 0.8855 (t0) cc_final: 0.8188 (t0) REVERT: U 78 ARG cc_start: 0.8544 (tpt90) cc_final: 0.8306 (tpt-90) REVERT: U 87 GLU cc_start: 0.8044 (pt0) cc_final: 0.7483 (pt0) REVERT: U 92 GLN cc_start: 0.8955 (tt0) cc_final: 0.8519 (tt0) REVERT: U 98 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: U 111 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8033 (p0) REVERT: U 123 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6567 (mt-10) REVERT: V 4 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8059 (mm-40) REVERT: V 27 LEU cc_start: 0.9416 (pt) cc_final: 0.9204 (pt) REVERT: V 28 ARG cc_start: 0.8581 (mtm180) cc_final: 0.7153 (mmp-170) REVERT: V 76 ASP cc_start: 0.8300 (t0) cc_final: 0.7940 (t0) REVERT: V 98 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: V 100 ILE cc_start: 0.8937 (mm) cc_final: 0.8574 (mm) REVERT: W 37 GLU cc_start: 0.7920 (tp30) cc_final: 0.7633 (tp30) REVERT: W 77 GLU cc_start: 0.9202 (tp30) cc_final: 0.8843 (tp30) REVERT: W 98 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: W 134 PHE cc_start: 0.8559 (t80) cc_final: 0.8246 (t80) REVERT: X 8 ASP cc_start: 0.7886 (m-30) cc_final: 0.7465 (m-30) REVERT: X 28 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8579 (mtm180) REVERT: X 98 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7557 (m-80) outliers start: 173 outliers final: 130 residues processed: 802 average time/residue: 0.3324 time to fit residues: 419.4313 Evaluate side-chains 867 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 708 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 92 GLN Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 126 MET Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 98 PHE Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 111 ASP Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain O residue 126 MET Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 98 PHE Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain U residue 126 MET Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 37 GLU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 0.2980 chunk 205 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 117 ASN G 92 GLN J 47 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 117 ASN S 92 GLN V 47 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24216 Z= 0.286 Angle : 0.786 13.342 32712 Z= 0.387 Chirality : 0.052 0.319 3648 Planarity : 0.003 0.031 4368 Dihedral : 5.692 23.749 3384 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.56 % Allowed : 29.41 % Favored : 64.03 % 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: -2.78 (0.13), residues: 3168 helix: -0.98 (0.23), residues: 480 sheet: -1.05 (0.14), residues: 1176 loop : -2.83 (0.13), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 50 HIS 0.005 0.001 HIS P 116 PHE 0.019 0.002 PHE D 21 TYR 0.011 0.001 TYR W 112 ARG 0.005 0.001 ARG W 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 718 time to evaluate : 2.628 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: B 33 SER cc_start: 0.9232 (t) cc_final: 0.8613 (p) REVERT: B 35 ASN cc_start: 0.8660 (m-40) cc_final: 0.8068 (m110) REVERT: B 47 GLN cc_start: 0.8593 (pm20) cc_final: 0.8320 (pm20) REVERT: B 76 ASP cc_start: 0.8842 (t0) cc_final: 0.8449 (t0) REVERT: B 92 GLN cc_start: 0.9004 (tt0) cc_final: 0.8445 (tt0) REVERT: B 98 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: B 111 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7926 (p0) REVERT: A 12 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8361 (mtpp) REVERT: A 28 ARG cc_start: 0.8573 (mtm180) cc_final: 0.7059 (mmp-170) REVERT: A 76 ASP cc_start: 0.8183 (t0) cc_final: 0.7824 (t0) REVERT: A 85 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7198 (p0) REVERT: A 98 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: C 77 GLU cc_start: 0.9165 (tp30) cc_final: 0.8836 (tp30) REVERT: C 98 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8194 (m-10) REVERT: C 110 ILE cc_start: 0.8930 (tp) cc_final: 0.8692 (tp) REVERT: D 8 ASP cc_start: 0.7903 (m-30) cc_final: 0.7642 (m-30) REVERT: D 71 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8561 (mtmm) REVERT: D 76 ASP cc_start: 0.8194 (t0) cc_final: 0.7864 (t0) REVERT: D 98 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: E 76 ASP cc_start: 0.8891 (t0) cc_final: 0.8482 (t0) REVERT: E 98 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: E 134 PHE cc_start: 0.8670 (t80) cc_final: 0.8238 (t80) REVERT: F 4 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8237 (mm-40) REVERT: F 28 ARG cc_start: 0.8690 (mtm180) cc_final: 0.7097 (mmp-170) REVERT: F 98 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: G 76 ASP cc_start: 0.8580 (t0) cc_final: 0.8241 (t0) REVERT: G 98 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: H 50 TRP cc_start: 0.8223 (m100) cc_final: 0.8006 (m100) REVERT: H 76 ASP cc_start: 0.8173 (t0) cc_final: 0.7810 (t0) REVERT: H 98 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: I 35 ASN cc_start: 0.8574 (m110) cc_final: 0.8002 (m-40) REVERT: I 76 ASP cc_start: 0.8832 (t0) cc_final: 0.8171 (t0) REVERT: I 87 GLU cc_start: 0.7977 (pt0) cc_final: 0.7442 (pt0) REVERT: I 92 GLN cc_start: 0.8940 (tt0) cc_final: 0.8567 (tt0) REVERT: I 111 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8051 (p0) REVERT: J 4 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8079 (mm-40) REVERT: J 27 LEU cc_start: 0.9391 (pt) cc_final: 0.9175 (pt) REVERT: J 28 ARG cc_start: 0.8581 (mtm180) cc_final: 0.7110 (mmp-170) REVERT: J 76 ASP cc_start: 0.8290 (t0) cc_final: 0.7912 (t0) REVERT: J 98 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: J 100 ILE cc_start: 0.8939 (mm) cc_final: 0.8581 (mm) REVERT: K 37 GLU cc_start: 0.7909 (tp30) cc_final: 0.7607 (tp30) REVERT: K 77 GLU cc_start: 0.9224 (tp30) cc_final: 0.8917 (tp30) REVERT: K 92 GLN cc_start: 0.8804 (tt0) cc_final: 0.8459 (tt0) REVERT: K 98 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7945 (m-10) REVERT: L 7 LYS cc_start: 0.9285 (ptmm) cc_final: 0.9051 (ptmm) REVERT: L 22 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7213 (mm-30) REVERT: L 28 ARG cc_start: 0.8781 (mtm180) cc_final: 0.8570 (mtm180) REVERT: M 33 SER cc_start: 0.9229 (t) cc_final: 0.8631 (p) REVERT: M 35 ASN cc_start: 0.8663 (m-40) cc_final: 0.8060 (m110) REVERT: M 47 GLN cc_start: 0.8623 (pm20) cc_final: 0.8352 (pm20) REVERT: M 76 ASP cc_start: 0.8840 (t0) cc_final: 0.8445 (t0) REVERT: M 92 GLN cc_start: 0.9014 (tt0) cc_final: 0.8452 (tt0) REVERT: M 98 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.7214 (m-10) REVERT: M 111 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7931 (p0) REVERT: N 12 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8370 (mtpp) REVERT: N 28 ARG cc_start: 0.8596 (mtm180) cc_final: 0.7063 (mmp-170) REVERT: N 76 ASP cc_start: 0.8177 (t0) cc_final: 0.7717 (t0) REVERT: N 85 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7270 (p0) REVERT: N 98 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: O 98 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8200 (m-10) REVERT: O 110 ILE cc_start: 0.8931 (tp) cc_final: 0.8693 (tp) REVERT: Q 76 ASP cc_start: 0.8869 (t0) cc_final: 0.8447 (t0) REVERT: Q 98 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: Q 134 PHE cc_start: 0.8676 (t80) cc_final: 0.8245 (t80) REVERT: R 4 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8246 (mm-40) REVERT: R 28 ARG cc_start: 0.8720 (mtm180) cc_final: 0.7125 (mmp-170) REVERT: R 98 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: S 76 ASP cc_start: 0.8559 (t0) cc_final: 0.8236 (t0) REVERT: S 98 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: T 23 THR cc_start: 0.8646 (m) cc_final: 0.8244 (p) REVERT: T 50 TRP cc_start: 0.8230 (m100) cc_final: 0.7985 (m100) REVERT: T 76 ASP cc_start: 0.8137 (t0) cc_final: 0.7877 (t0) REVERT: T 98 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: U 35 ASN cc_start: 0.8549 (m110) cc_final: 0.7990 (m-40) REVERT: U 76 ASP cc_start: 0.8832 (t0) cc_final: 0.8171 (t0) REVERT: U 87 GLU cc_start: 0.7980 (pt0) cc_final: 0.7442 (pt0) REVERT: U 92 GLN cc_start: 0.8925 (tt0) cc_final: 0.8560 (tt0) REVERT: U 111 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8037 (p0) REVERT: V 4 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8037 (mm-40) REVERT: V 28 ARG cc_start: 0.8592 (mtm180) cc_final: 0.7107 (mmp-170) REVERT: V 76 ASP cc_start: 0.8293 (t0) cc_final: 0.7911 (t0) REVERT: V 98 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: V 100 ILE cc_start: 0.8925 (mm) cc_final: 0.8562 (mm) REVERT: W 37 GLU cc_start: 0.7911 (tp30) cc_final: 0.7611 (tp30) REVERT: W 77 GLU cc_start: 0.9214 (tp30) cc_final: 0.8890 (tp30) REVERT: W 90 GLU cc_start: 0.7594 (tp30) cc_final: 0.7291 (tp30) REVERT: W 98 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: W 134 PHE cc_start: 0.8450 (t80) cc_final: 0.8208 (t80) REVERT: X 28 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8560 (mtm180) REVERT: X 45 GLU cc_start: 0.7642 (pp20) cc_final: 0.7422 (pp20) REVERT: X 98 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7508 (m-80) outliers start: 159 outliers final: 119 residues processed: 790 average time/residue: 0.3277 time to fit residues: 408.6424 Evaluate side-chains 848 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 701 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 98 PHE Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 98 PHE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 PHE Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 111 ASP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 98 PHE Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 98 PHE Chi-restraints excluded: chain M residue 111 ASP Chi-restraints excluded: chain N residue 12 LYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain O residue 13 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 98 PHE Chi-restraints excluded: chain O residue 111 ASP Chi-restraints excluded: chain O residue 115 SER Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 32 ILE Chi-restraints excluded: chain P residue 42 THR Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 111 ASP Chi-restraints excluded: chain Q residue 98 PHE Chi-restraints excluded: chain Q residue 124 LEU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain S residue 98 PHE Chi-restraints excluded: chain S residue 110 ILE Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 13 LEU Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 24 ILE Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 42 THR Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 97 ASP Chi-restraints excluded: chain T residue 98 PHE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain T residue 111 ASP Chi-restraints excluded: chain U residue 14 ASP Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 111 ASP Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 98 PHE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 111 ASP Chi-restraints excluded: chain V residue 126 MET Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 98 PHE Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain W residue 115 SER Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 37 GLU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN D 92 GLN ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN F 117 ASN ** H 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 47 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN R 117 ASN S 92 GLN U 47 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.085057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.073490 restraints weight = 48779.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.076010 restraints weight = 23077.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077655 restraints weight = 13170.678| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 24216 Z= 0.456 Angle : 0.853 14.228 32712 Z= 0.429 Chirality : 0.055 0.346 3648 Planarity : 0.004 0.038 4368 Dihedral : 6.080 24.335 3384 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 6.77 % Allowed : 29.37 % Favored : 63.86 % 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: -2.87 (0.13), residues: 3168 helix: -1.04 (0.23), residues: 480 sheet: -1.31 (0.14), residues: 1200 loop : -2.70 (0.13), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 50 HIS 0.005 0.001 HIS P 116 PHE 0.028 0.002 PHE D 21 TYR 0.014 0.002 TYR W 112 ARG 0.006 0.001 ARG U 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7050.66 seconds wall clock time: 126 minutes 5.14 seconds (7565.14 seconds total)