Starting phenix.real_space_refine on Sun Feb 18 11:03:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwk_10040/02_2024/6rwk_10040.pdb" } resolution = 3.86 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= 0.009 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 32 5.16 5 C 14224 2.51 5 N 3408 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 138": "NH1" <-> "NH2" Residue "0 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 138": "NH1" <-> "NH2" Residue "2 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 138": "NH1" <-> "NH2" Residue "4 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 138": "NH1" <-> "NH2" Residue "8 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 70": "NH1" <-> "NH2" Residue "x TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 138": "NH1" <-> "NH2" Residue "x PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 70": "NH1" <-> "NH2" Residue "y PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 138": "NH1" <-> "NH2" Residue "y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 70": "NH1" <-> "NH2" Residue "z TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 138": "NH1" <-> "NH2" Residue "z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 70": "NH1" <-> "NH2" Residue "1 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 138": "NH1" <-> "NH2" Residue "1 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 70": "NH1" <-> "NH2" Residue "3 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 138": "NH1" <-> "NH2" Residue "3 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 70": "NH1" <-> "NH2" Residue "5 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 138": "NH1" <-> "NH2" Residue "5 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 70": "NH1" <-> "NH2" Residue "7 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 138": "NH1" <-> "NH2" Residue "7 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 70": "NH1" <-> "NH2" Residue "9 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 138": "NH1" <-> "NH2" Residue "9 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21760 Number of models: 1 Model: "" Number of chains: 32 Chain: "X" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Y" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Z" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "0" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "2" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "4" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "6" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "8" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "x" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "y" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "z" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "1" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "3" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "5" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "7" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "9" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1102 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "P" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "S" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "U" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "K" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "N" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "Q" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "T" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "V" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 258 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Time building chain proxies: 11.18, per 1000 atoms: 0.51 Number of scatterers: 21760 At special positions: 0 Unit cell: (170.194, 170.194, 88.5562, 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 32 16.00 O 4096 8.00 N 3408 7.00 C 14224 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: 8.31 Conformation dependent library (CDL) restraints added in 3.7 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 33 sheets defined 34.2% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'X' and resid 45 through 57 Processing helix chain 'X' and resid 65 through 68 Processing helix chain 'X' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET X 83 " --> pdb=" O ASN X 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 110 No H-bonds generated for 'chain 'X' and resid 108 through 110' Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 155 through 168 Processing helix chain 'Y' and resid 45 through 57 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET Y 83 " --> pdb=" O ASN Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 110 No H-bonds generated for 'chain 'Y' and resid 108 through 110' Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 155 through 168 Processing helix chain 'Z' and resid 45 through 57 Processing helix chain 'Z' and resid 65 through 68 Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET Z 83 " --> pdb=" O ASN Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 110 No H-bonds generated for 'chain 'Z' and resid 108 through 110' Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 155 through 168 Processing helix chain '0' and resid 45 through 57 Processing helix chain '0' and resid 65 through 68 Processing helix chain '0' and resid 79 through 91 removed outlier: 3.842A pdb=" N MET 0 83 " --> pdb=" O ASN 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 108 through 110 No H-bonds generated for 'chain '0' and resid 108 through 110' Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 155 through 168 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 65 through 68 Processing helix chain '2' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET 2 83 " --> pdb=" O ASN 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 110 No H-bonds generated for 'chain '2' and resid 108 through 110' Processing helix chain '2' and resid 121 through 132 Processing helix chain '2' and resid 155 through 168 Processing helix chain '4' and resid 45 through 57 Processing helix chain '4' and resid 65 through 68 Processing helix chain '4' and resid 79 through 91 removed outlier: 3.842A pdb=" N MET 4 83 " --> pdb=" O ASN 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 108 through 110 No H-bonds generated for 'chain '4' and resid 108 through 110' Processing helix chain '4' and resid 121 through 132 Processing helix chain '4' and resid 155 through 168 Processing helix chain '6' and resid 45 through 57 Processing helix chain '6' and resid 65 through 68 Processing helix chain '6' and resid 79 through 91 removed outlier: 3.843A pdb=" N MET 6 83 " --> pdb=" O ASN 6 79 " (cutoff:3.500A) Processing helix chain '6' and resid 108 through 110 No H-bonds generated for 'chain '6' and resid 108 through 110' Processing helix chain '6' and resid 121 through 132 Processing helix chain '6' and resid 155 through 168 Processing helix chain '8' and resid 45 through 57 Processing helix chain '8' and resid 65 through 68 Processing helix chain '8' and resid 79 through 91 removed outlier: 3.844A pdb=" N MET 8 83 " --> pdb=" O ASN 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 110 No H-bonds generated for 'chain '8' and resid 108 through 110' Processing helix chain '8' and resid 121 through 132 Processing helix chain '8' and resid 155 through 168 Processing helix chain 'x' and resid 45 through 57 Processing helix chain 'x' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET x 83 " --> pdb=" O ASN x 79 " (cutoff:3.500A) Processing helix chain 'x' and resid 108 through 110 No H-bonds generated for 'chain 'x' and resid 108 through 110' Processing helix chain 'x' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU x 125 " --> pdb=" O SER x 121 " (cutoff:3.500A) Processing helix chain 'x' and resid 155 through 168 Processing helix chain 'y' and resid 45 through 57 Processing helix chain 'y' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET y 83 " --> pdb=" O ASN y 79 " (cutoff:3.500A) Processing helix chain 'y' and resid 108 through 110 No H-bonds generated for 'chain 'y' and resid 108 through 110' Processing helix chain 'y' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU y 125 " --> pdb=" O SER y 121 " (cutoff:3.500A) Processing helix chain 'y' and resid 155 through 168 Processing helix chain 'z' and resid 45 through 57 Processing helix chain 'z' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET z 83 " --> pdb=" O ASN z 79 " (cutoff:3.500A) Processing helix chain 'z' and resid 108 through 110 No H-bonds generated for 'chain 'z' and resid 108 through 110' Processing helix chain 'z' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU z 125 " --> pdb=" O SER z 121 " (cutoff:3.500A) Processing helix chain 'z' and resid 155 through 168 Processing helix chain '1' and resid 45 through 57 Processing helix chain '1' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET 1 83 " --> pdb=" O ASN 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 108 through 110 No H-bonds generated for 'chain '1' and resid 108 through 110' Processing helix chain '1' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 1 125 " --> pdb=" O SER 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 155 through 168 Processing helix chain '3' and resid 45 through 57 Processing helix chain '3' and resid 79 through 92 removed outlier: 3.605A pdb=" N MET 3 83 " --> pdb=" O ASN 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 110 No H-bonds generated for 'chain '3' and resid 108 through 110' Processing helix chain '3' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 3 125 " --> pdb=" O SER 3 121 " (cutoff:3.500A) Processing helix chain '3' and resid 155 through 168 Processing helix chain '5' and resid 45 through 57 Processing helix chain '5' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 5 83 " --> pdb=" O ASN 5 79 " (cutoff:3.500A) Processing helix chain '5' and resid 108 through 110 No H-bonds generated for 'chain '5' and resid 108 through 110' Processing helix chain '5' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 5 125 " --> pdb=" O SER 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 155 through 168 Processing helix chain '7' and resid 45 through 57 Processing helix chain '7' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 7 83 " --> pdb=" O ASN 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 121 through 132 removed outlier: 3.541A pdb=" N LEU 7 125 " --> pdb=" O SER 7 121 " (cutoff:3.500A) Processing helix chain '7' and resid 155 through 168 Processing helix chain '9' and resid 45 through 57 Processing helix chain '9' and resid 79 through 92 removed outlier: 3.604A pdb=" N MET 9 83 " --> pdb=" O ASN 9 79 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 110 No H-bonds generated for 'chain '9' and resid 108 through 110' Processing helix chain '9' and resid 121 through 132 removed outlier: 3.542A pdb=" N LEU 9 125 " --> pdb=" O SER 9 121 " (cutoff:3.500A) Processing helix chain '9' and resid 155 through 168 Processing sheet with id=AA1, first strand: chain 'X' and resid 37 through 44 removed outlier: 4.537A pdb=" N SER X 42 " --> pdb=" O ILE X 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE X 71 " --> pdb=" O SER X 42 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG X 70 " --> pdb=" O TRP E 364 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE E 366 " --> pdb=" O ARG X 70 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER X 72 " --> pdb=" O PHE E 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER x 42 " --> pdb=" O ILE x 71 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE x 71 " --> pdb=" O SER x 42 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG x 70 " --> pdb=" O TRP G 364 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE G 366 " --> pdb=" O ARG x 70 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER x 72 " --> pdb=" O PHE G 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Y 42 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Y 71 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG Y 70 " --> pdb=" O TRP H 364 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE H 366 " --> pdb=" O ARG Y 70 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER Y 72 " --> pdb=" O PHE H 366 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 349 " --> pdb=" O VAL y 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER y 42 " --> pdb=" O ILE y 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE y 71 " --> pdb=" O SER y 42 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG y 70 " --> pdb=" O TRP J 364 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE J 366 " --> pdb=" O ARG y 70 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER y 72 " --> pdb=" O PHE J 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Z 42 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE Z 71 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ARG Z 70 " --> pdb=" O TRP K 364 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N PHE K 366 " --> pdb=" O ARG Z 70 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Z 72 " --> pdb=" O PHE K 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER z 42 " --> pdb=" O ILE z 71 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE z 71 " --> pdb=" O SER z 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG z 70 " --> pdb=" O TRP M 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE M 366 " --> pdb=" O ARG z 70 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER z 72 " --> pdb=" O PHE M 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 0 42 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 0 71 " --> pdb=" O SER 0 42 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG 0 70 " --> pdb=" O TRP N 364 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE N 366 " --> pdb=" O ARG 0 70 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER 0 72 " --> pdb=" O PHE N 366 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR N 349 " --> pdb=" O VAL 1 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 1 42 " --> pdb=" O ILE 1 71 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE 1 71 " --> pdb=" O SER 1 42 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG 1 70 " --> pdb=" O TRP P 364 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE P 366 " --> pdb=" O ARG 1 70 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER 1 72 " --> pdb=" O PHE P 366 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER 2 42 " --> pdb=" O ILE 2 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 2 71 " --> pdb=" O SER 2 42 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG 2 70 " --> pdb=" O TRP Q 364 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE Q 366 " --> pdb=" O ARG 2 70 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER 2 72 " --> pdb=" O PHE Q 366 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR Q 349 " --> pdb=" O VAL 3 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 3 42 " --> pdb=" O ILE 3 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 3 71 " --> pdb=" O SER 3 42 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG 3 70 " --> pdb=" O TRP S 364 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE S 366 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER 3 72 " --> pdb=" O PHE S 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 4 42 " --> pdb=" O ILE 4 71 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE 4 71 " --> pdb=" O SER 4 42 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG 4 70 " --> pdb=" O TRP T 364 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE T 366 " --> pdb=" O ARG 4 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER 4 72 " --> pdb=" O PHE T 366 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR T 349 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER 5 42 " --> pdb=" O ILE 5 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 5 71 " --> pdb=" O SER 5 42 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG 5 70 " --> pdb=" O TRP U 364 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE U 366 " --> pdb=" O ARG 5 70 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER 5 72 " --> pdb=" O PHE U 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 6 42 " --> pdb=" O ILE 6 71 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE 6 71 " --> pdb=" O SER 6 42 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG 6 70 " --> pdb=" O TRP V 364 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE V 366 " --> pdb=" O ARG 6 70 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER 6 72 " --> pdb=" O PHE V 366 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR V 349 " --> pdb=" O VAL 7 39 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 7 42 " --> pdb=" O ILE 7 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 7 71 " --> pdb=" O SER 7 42 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG 7 70 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE A 366 " --> pdb=" O ARG 7 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER 7 72 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER 8 42 " --> pdb=" O ILE 8 71 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE 8 71 " --> pdb=" O SER 8 42 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG 8 70 " --> pdb=" O TRP B 364 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE B 366 " --> pdb=" O ARG 8 70 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER 8 72 " --> pdb=" O PHE B 366 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 9 42 " --> pdb=" O ILE 9 71 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE 9 71 " --> pdb=" O SER 9 42 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG 9 70 " --> pdb=" O TRP D 364 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE D 366 " --> pdb=" O ARG 9 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER 9 72 " --> pdb=" O PHE D 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'X' and resid 111 through 116 Processing sheet with id=AA4, first strand: chain 'Y' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'Y' and resid 111 through 116 Processing sheet with id=AA6, first strand: chain 'Z' and resid 60 through 62 Processing sheet with id=AA7, first strand: chain 'Z' and resid 111 through 116 Processing sheet with id=AA8, first strand: chain '0' and resid 60 through 62 Processing sheet with id=AA9, first strand: chain '0' and resid 111 through 116 Processing sheet with id=AB1, first strand: chain '2' and resid 60 through 62 Processing sheet with id=AB2, first strand: chain '2' and resid 111 through 116 Processing sheet with id=AB3, first strand: chain '4' and resid 60 through 62 Processing sheet with id=AB4, first strand: chain '4' and resid 111 through 116 Processing sheet with id=AB5, first strand: chain '6' and resid 60 through 62 Processing sheet with id=AB6, first strand: chain '6' and resid 111 through 116 Processing sheet with id=AB7, first strand: chain '8' and resid 60 through 62 Processing sheet with id=AB8, first strand: chain '8' and resid 111 through 116 Processing sheet with id=AB9, first strand: chain 'x' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL x 61 " --> pdb=" O ILE x 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP x 106 " --> pdb=" O VAL x 61 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'x' and resid 111 through 116 Processing sheet with id=AC2, first strand: chain 'y' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL y 61 " --> pdb=" O ILE y 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP y 106 " --> pdb=" O VAL y 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'y' and resid 111 through 116 Processing sheet with id=AC4, first strand: chain 'z' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL z 61 " --> pdb=" O ILE z 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP z 106 " --> pdb=" O VAL z 61 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'z' and resid 111 through 116 Processing sheet with id=AC6, first strand: chain '1' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 1 61 " --> pdb=" O ILE 1 104 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP 1 106 " --> pdb=" O VAL 1 61 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '1' and resid 111 through 116 Processing sheet with id=AC8, first strand: chain '3' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 3 61 " --> pdb=" O ILE 3 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 3 106 " --> pdb=" O VAL 3 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 111 through 116 Processing sheet with id=AD1, first strand: chain '5' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 5 61 " --> pdb=" O ILE 5 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 5 106 " --> pdb=" O VAL 5 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '5' and resid 111 through 116 Processing sheet with id=AD3, first strand: chain '7' and resid 61 through 62 removed outlier: 6.786A pdb=" N VAL 7 61 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 7 106 " --> pdb=" O VAL 7 61 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 111 through 116 Processing sheet with id=AD5, first strand: chain '9' and resid 61 through 62 removed outlier: 6.787A pdb=" N VAL 9 61 " --> pdb=" O ILE 9 104 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP 9 106 " --> pdb=" O VAL 9 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '9' and resid 111 through 116 1021 hydrogen bonds defined for protein. 2784 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: 7.30 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6720 1.34 - 1.45: 3854 1.45 - 1.57: 11586 1.57 - 1.68: 0 1.68 - 1.80: 64 Bond restraints: 22224 Sorted by residual: bond pdb=" C PRO x 140 " pdb=" O PRO x 140 " ideal model delta sigma weight residual 1.235 1.255 -0.020 1.30e-02 5.92e+03 2.38e+00 bond pdb=" C PRO z 140 " pdb=" O PRO z 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO y 140 " pdb=" O PRO y 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO 9 140 " pdb=" O PRO 9 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 bond pdb=" C PRO 7 140 " pdb=" O PRO 7 140 " ideal model delta sigma weight residual 1.235 1.254 -0.019 1.30e-02 5.92e+03 2.19e+00 ... (remaining 22219 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.37: 264 105.37 - 112.53: 11855 112.53 - 119.70: 7052 119.70 - 126.86: 10712 126.86 - 134.02: 197 Bond angle restraints: 30080 Sorted by residual: angle pdb=" CA PRO 6 140 " pdb=" C PRO 6 140 " pdb=" N ILE 6 141 " ideal model delta sigma weight residual 116.70 109.85 6.85 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 2 140 " pdb=" C PRO 2 140 " pdb=" N ILE 2 141 " ideal model delta sigma weight residual 116.70 109.85 6.85 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 0 140 " pdb=" C PRO 0 140 " pdb=" N ILE 0 141 " ideal model delta sigma weight residual 116.70 109.86 6.84 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO Y 140 " pdb=" C PRO Y 140 " pdb=" N ILE Y 141 " ideal model delta sigma weight residual 116.70 109.87 6.83 2.07e+00 2.33e-01 1.09e+01 angle pdb=" CA PRO 4 140 " pdb=" C PRO 4 140 " pdb=" N ILE 4 141 " ideal model delta sigma weight residual 116.70 109.88 6.82 2.07e+00 2.33e-01 1.09e+01 ... (remaining 30075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 10852 11.41 - 22.83: 1604 22.83 - 34.24: 489 34.24 - 45.65: 175 45.65 - 57.06: 128 Dihedral angle restraints: 13248 sinusoidal: 5280 harmonic: 7968 Sorted by residual: dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP S 341 " pdb=" C ASP S 341 " pdb=" N ASP S 342 " pdb=" CA ASP S 342 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP U 341 " pdb=" C ASP U 341 " pdb=" N ASP U 342 " pdb=" CA ASP U 342 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2045 0.034 - 0.068: 873 0.068 - 0.102: 311 0.102 - 0.135: 131 0.135 - 0.169: 32 Chirality restraints: 3392 Sorted by residual: chirality pdb=" CA PRO Y 140 " pdb=" N PRO Y 140 " pdb=" C PRO Y 140 " pdb=" CB PRO Y 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA PRO X 140 " pdb=" N PRO X 140 " pdb=" C PRO X 140 " pdb=" CB PRO X 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA PRO 6 140 " pdb=" N PRO 6 140 " pdb=" C PRO 6 140 " pdb=" CB PRO 6 140 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 3389 not shown) Planarity restraints: 3744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 3 139 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO 3 140 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO 3 140 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 3 140 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR z 139 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO z 140 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO z 140 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO z 140 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR Z 139 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO Z 140 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO Z 140 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO Z 140 " -0.028 5.00e-02 4.00e+02 ... (remaining 3741 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1576 2.73 - 3.27: 22031 3.27 - 3.81: 34195 3.81 - 4.36: 39761 4.36 - 4.90: 70636 Nonbonded interactions: 168199 Sorted by model distance: nonbonded pdb=" OG SER 4 47 " pdb=" NH1 ARG 4 51 " model vdw 2.183 2.520 nonbonded pdb=" OG SER Z 47 " pdb=" NH1 ARG Z 51 " model vdw 2.184 2.520 nonbonded pdb=" OG SER 0 47 " pdb=" NH1 ARG 0 51 " model vdw 2.184 2.520 nonbonded pdb=" OG SER 2 47 " pdb=" NH1 ARG 2 51 " model vdw 2.184 2.520 nonbonded pdb=" OG SER X 47 " pdb=" NH1 ARG X 51 " model vdw 2.184 2.520 ... (remaining 168194 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.480 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 56.900 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.007 0.034 22224 Z= 0.449 Angle : 0.757 6.848 30080 Z= 0.403 Chirality : 0.046 0.169 3392 Planarity : 0.005 0.050 3744 Dihedral : 13.644 57.064 8128 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 5.83 % Allowed : 10.50 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.14), residues: 2624 helix: -1.48 (0.16), residues: 928 sheet: -2.44 (0.17), residues: 752 loop : -3.75 (0.14), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 364 HIS 0.003 0.001 HIS S 363 PHE 0.010 0.002 PHE U 366 TYR 0.014 0.002 TYR 2 151 ARG 0.003 0.001 ARG 6 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1030 time to evaluate : 2.548 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: X 68 LYS cc_start: 0.9387 (mttt) cc_final: 0.9184 (mttp) REVERT: X 85 GLU cc_start: 0.8561 (tp30) cc_final: 0.8225 (tm-30) REVERT: X 88 THR cc_start: 0.9574 (m) cc_final: 0.9249 (p) REVERT: X 106 ASP cc_start: 0.8447 (t0) cc_final: 0.8051 (t0) REVERT: X 117 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8395 (pp) REVERT: X 133 ASN cc_start: 0.9082 (m-40) cc_final: 0.8251 (t0) REVERT: X 144 ASN cc_start: 0.8769 (t0) cc_final: 0.8424 (t0) REVERT: Y 37 LYS cc_start: 0.9197 (tttt) cc_final: 0.8039 (tptm) REVERT: Y 88 THR cc_start: 0.9625 (m) cc_final: 0.9324 (p) REVERT: Y 97 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8717 (tttm) REVERT: Y 106 ASP cc_start: 0.8465 (t0) cc_final: 0.8165 (t0) REVERT: Y 117 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8155 (pp) REVERT: Y 133 ASN cc_start: 0.9143 (m-40) cc_final: 0.8691 (t0) REVERT: Y 144 ASN cc_start: 0.8694 (t0) cc_final: 0.8310 (t0) REVERT: Z 68 LYS cc_start: 0.9394 (mttt) cc_final: 0.9159 (mttp) REVERT: Z 85 GLU cc_start: 0.8555 (tp30) cc_final: 0.8255 (tm-30) REVERT: Z 88 THR cc_start: 0.9579 (m) cc_final: 0.9262 (p) REVERT: Z 106 ASP cc_start: 0.8452 (t0) cc_final: 0.8063 (t0) REVERT: Z 117 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (pp) REVERT: Z 133 ASN cc_start: 0.9085 (m-40) cc_final: 0.8246 (t0) REVERT: Z 144 ASN cc_start: 0.8778 (t0) cc_final: 0.8439 (t0) REVERT: 0 88 THR cc_start: 0.9649 (m) cc_final: 0.9362 (p) REVERT: 0 97 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8759 (tttm) REVERT: 0 106 ASP cc_start: 0.8498 (t0) cc_final: 0.8215 (t0) REVERT: 0 117 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.7905 (pp) REVERT: 0 133 ASN cc_start: 0.9130 (m-40) cc_final: 0.8588 (t0) REVERT: 0 144 ASN cc_start: 0.8648 (t0) cc_final: 0.8281 (t0) REVERT: 2 68 LYS cc_start: 0.9395 (mttt) cc_final: 0.9167 (mttp) REVERT: 2 85 GLU cc_start: 0.8570 (tp30) cc_final: 0.8316 (tm-30) REVERT: 2 88 THR cc_start: 0.9596 (m) cc_final: 0.9293 (p) REVERT: 2 106 ASP cc_start: 0.8492 (t0) cc_final: 0.8172 (t0) REVERT: 2 117 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8385 (pp) REVERT: 2 133 ASN cc_start: 0.9100 (m-40) cc_final: 0.8274 (t0) REVERT: 2 144 ASN cc_start: 0.8789 (t0) cc_final: 0.8423 (t0) REVERT: 4 88 THR cc_start: 0.9669 (m) cc_final: 0.9427 (p) REVERT: 4 97 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8781 (tttm) REVERT: 4 106 ASP cc_start: 0.8506 (t0) cc_final: 0.8232 (t0) REVERT: 4 117 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7938 (pp) REVERT: 4 133 ASN cc_start: 0.9069 (m-40) cc_final: 0.8494 (t0) REVERT: 4 144 ASN cc_start: 0.8648 (t0) cc_final: 0.8283 (t0) REVERT: 6 68 LYS cc_start: 0.9403 (mttt) cc_final: 0.9156 (mttp) REVERT: 6 85 GLU cc_start: 0.8564 (tp30) cc_final: 0.8310 (tm-30) REVERT: 6 88 THR cc_start: 0.9594 (m) cc_final: 0.9290 (p) REVERT: 6 106 ASP cc_start: 0.8474 (t0) cc_final: 0.8157 (t0) REVERT: 6 117 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8396 (pp) REVERT: 6 133 ASN cc_start: 0.9094 (m-40) cc_final: 0.8267 (t0) REVERT: 6 144 ASN cc_start: 0.8781 (t0) cc_final: 0.8430 (t0) REVERT: 8 37 LYS cc_start: 0.9165 (tttt) cc_final: 0.7829 (tptm) REVERT: 8 88 THR cc_start: 0.9599 (m) cc_final: 0.9286 (p) REVERT: 8 97 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8630 (tttm) REVERT: 8 106 ASP cc_start: 0.8441 (t0) cc_final: 0.8157 (t0) REVERT: 8 117 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7919 (pp) REVERT: 8 133 ASN cc_start: 0.9089 (m-40) cc_final: 0.8648 (t0) REVERT: 8 144 ASN cc_start: 0.8696 (t0) cc_final: 0.8367 (t0) REVERT: x 37 LYS cc_start: 0.8946 (mttt) cc_final: 0.8643 (tttt) REVERT: x 70 ARG cc_start: 0.8707 (mtt-85) cc_final: 0.8268 (mtt-85) REVERT: x 85 GLU cc_start: 0.8449 (tp30) cc_final: 0.8078 (tm-30) REVERT: x 86 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8367 (ttpp) REVERT: x 97 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8387 (tttp) REVERT: x 109 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7736 (mt-10) REVERT: x 117 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8158 (pp) REVERT: x 120 ILE cc_start: 0.9132 (mt) cc_final: 0.8796 (mm) REVERT: x 138 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8295 (mtm-85) REVERT: y 48 PHE cc_start: 0.9212 (t80) cc_final: 0.8869 (t80) REVERT: y 51 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: y 58 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6983 (m-10) REVERT: y 82 GLU cc_start: 0.8487 (mp0) cc_final: 0.8264 (mp0) REVERT: y 84 LEU cc_start: 0.9321 (tp) cc_final: 0.8942 (tp) REVERT: y 85 GLU cc_start: 0.8609 (tp30) cc_final: 0.8256 (tm-30) REVERT: y 86 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8636 (ttpp) REVERT: y 97 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8489 (tttm) REVERT: y 109 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7908 (mt-10) REVERT: y 117 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8225 (pp) REVERT: y 120 ILE cc_start: 0.9057 (mt) cc_final: 0.8515 (mp) REVERT: y 128 TYR cc_start: 0.9154 (t80) cc_final: 0.8915 (t80) REVERT: z 37 LYS cc_start: 0.8864 (mttt) cc_final: 0.8600 (ttmt) REVERT: z 74 GLU cc_start: 0.7914 (tt0) cc_final: 0.7382 (tt0) REVERT: z 82 GLU cc_start: 0.8704 (mp0) cc_final: 0.8372 (mp0) REVERT: z 85 GLU cc_start: 0.8515 (tp30) cc_final: 0.8055 (tm-30) REVERT: z 86 LYS cc_start: 0.9272 (ttpt) cc_final: 0.8378 (ttpp) REVERT: z 109 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7691 (mt-10) REVERT: z 117 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8304 (pp) REVERT: z 120 ILE cc_start: 0.9167 (mt) cc_final: 0.8930 (mp) REVERT: z 127 GLN cc_start: 0.9076 (tp40) cc_final: 0.8825 (tp-100) REVERT: z 138 ARG cc_start: 0.8642 (mtp-110) cc_final: 0.8312 (mtm-85) REVERT: 1 50 GLU cc_start: 0.8946 (tt0) cc_final: 0.8255 (tm-30) REVERT: 1 51 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: 1 58 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: 1 82 GLU cc_start: 0.8511 (mp0) cc_final: 0.8281 (mp0) REVERT: 1 84 LEU cc_start: 0.9303 (tp) cc_final: 0.8900 (tp) REVERT: 1 85 GLU cc_start: 0.8660 (tp30) cc_final: 0.8299 (tm-30) REVERT: 1 86 LYS cc_start: 0.9157 (ttpt) cc_final: 0.8770 (ttpp) REVERT: 1 97 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8498 (tttm) REVERT: 1 109 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7774 (mt-10) REVERT: 1 117 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8212 (pp) REVERT: 1 120 ILE cc_start: 0.9065 (mt) cc_final: 0.8528 (mp) REVERT: 3 37 LYS cc_start: 0.8949 (mttt) cc_final: 0.8630 (tttt) REVERT: 3 48 PHE cc_start: 0.9292 (t80) cc_final: 0.9074 (t80) REVERT: 3 65 GLN cc_start: 0.8849 (tt0) cc_final: 0.8594 (tm-30) REVERT: 3 70 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8328 (mtt-85) REVERT: 3 74 GLU cc_start: 0.7727 (tt0) cc_final: 0.7291 (tt0) REVERT: 3 85 GLU cc_start: 0.8405 (tp30) cc_final: 0.8104 (tm-30) REVERT: 3 86 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8747 (mtpt) REVERT: 3 97 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8414 (tttp) REVERT: 3 106 ASP cc_start: 0.8298 (t0) cc_final: 0.7945 (t0) REVERT: 3 117 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (pp) REVERT: 3 120 ILE cc_start: 0.9147 (mt) cc_final: 0.8820 (mm) REVERT: 3 138 ARG cc_start: 0.8575 (mtp-110) cc_final: 0.8299 (mtm-85) REVERT: 5 50 GLU cc_start: 0.8937 (tt0) cc_final: 0.8241 (tm-30) REVERT: 5 51 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.7060 (mtm-85) REVERT: 5 58 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: 5 82 GLU cc_start: 0.8502 (mp0) cc_final: 0.8273 (mp0) REVERT: 5 84 LEU cc_start: 0.9303 (tp) cc_final: 0.8917 (tp) REVERT: 5 85 GLU cc_start: 0.8668 (tp30) cc_final: 0.8297 (tm-30) REVERT: 5 86 LYS cc_start: 0.9152 (ttpt) cc_final: 0.8666 (ttpp) REVERT: 5 97 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8493 (tttm) REVERT: 5 109 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7900 (mt-10) REVERT: 5 117 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8211 (pp) REVERT: 5 120 ILE cc_start: 0.9066 (mt) cc_final: 0.8524 (mp) REVERT: 5 128 TYR cc_start: 0.9184 (t80) cc_final: 0.8978 (t80) REVERT: 7 37 LYS cc_start: 0.8880 (mttt) cc_final: 0.8572 (tttt) REVERT: 7 48 PHE cc_start: 0.9314 (t80) cc_final: 0.9093 (t80) REVERT: 7 65 GLN cc_start: 0.8857 (tt0) cc_final: 0.8570 (tm-30) REVERT: 7 70 ARG cc_start: 0.8719 (mtt-85) cc_final: 0.8277 (mtt-85) REVERT: 7 85 GLU cc_start: 0.8410 (tp30) cc_final: 0.8102 (tm-30) REVERT: 7 86 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8720 (mtpt) REVERT: 7 106 ASP cc_start: 0.8319 (t0) cc_final: 0.8060 (t0) REVERT: 7 117 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8222 (pp) REVERT: 7 120 ILE cc_start: 0.9144 (mt) cc_final: 0.8802 (mm) REVERT: 7 138 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8312 (mtm-85) REVERT: 9 48 PHE cc_start: 0.9221 (t80) cc_final: 0.8908 (t80) REVERT: 9 50 GLU cc_start: 0.8941 (tt0) cc_final: 0.8257 (tm-30) REVERT: 9 51 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.7165 (mtm-85) REVERT: 9 58 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: 9 82 GLU cc_start: 0.8495 (mp0) cc_final: 0.8266 (mp0) REVERT: 9 84 LEU cc_start: 0.9315 (tp) cc_final: 0.8937 (tp) REVERT: 9 85 GLU cc_start: 0.8679 (tp30) cc_final: 0.8312 (tm-30) REVERT: 9 86 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8607 (ttpp) REVERT: 9 97 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8476 (tttm) REVERT: 9 109 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7879 (mt-10) REVERT: 9 117 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8217 (pp) REVERT: 9 120 ILE cc_start: 0.9057 (mt) cc_final: 0.8513 (mp) REVERT: 9 128 TYR cc_start: 0.9183 (t80) cc_final: 0.8943 (t80) REVERT: A 359 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7270 (pp) REVERT: D 345 LYS cc_start: 0.8671 (mttt) cc_final: 0.8344 (tppp) REVERT: D 358 MET cc_start: 0.8448 (tpp) cc_final: 0.7652 (tpp) REVERT: D 359 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7469 (pp) REVERT: G 359 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7228 (pp) REVERT: J 358 MET cc_start: 0.8159 (tpp) cc_final: 0.7743 (tpp) REVERT: M 359 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7444 (pp) REVERT: P 358 MET cc_start: 0.8324 (tpp) cc_final: 0.7707 (tpp) REVERT: S 359 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7348 (pp) REVERT: U 345 LYS cc_start: 0.8656 (mttt) cc_final: 0.8265 (tppp) REVERT: U 356 TYR cc_start: 0.9492 (p90) cc_final: 0.9206 (p90) REVERT: U 358 MET cc_start: 0.8486 (tpp) cc_final: 0.7788 (tpp) REVERT: U 359 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7483 (pp) REVERT: B 358 MET cc_start: 0.8658 (tpp) cc_final: 0.8129 (tpp) REVERT: B 359 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8560 (pt) REVERT: E 345 LYS cc_start: 0.8156 (mttt) cc_final: 0.7949 (tmtt) REVERT: E 365 PHE cc_start: 0.8995 (t80) cc_final: 0.8753 (t80) REVERT: H 358 MET cc_start: 0.8668 (tpp) cc_final: 0.8156 (tpp) REVERT: H 359 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8575 (pt) REVERT: K 339 LEU cc_start: 0.9036 (mt) cc_final: 0.8681 (tt) REVERT: K 345 LYS cc_start: 0.8214 (mttt) cc_final: 0.8005 (tmtt) REVERT: K 365 PHE cc_start: 0.9012 (t80) cc_final: 0.8739 (t80) REVERT: N 358 MET cc_start: 0.8442 (tpp) cc_final: 0.8194 (ttm) REVERT: Q 353 LYS cc_start: 0.9025 (pttt) cc_final: 0.8808 (mmmt) REVERT: Q 358 MET cc_start: 0.8779 (tpp) cc_final: 0.8276 (tpp) REVERT: T 358 MET cc_start: 0.8620 (tpp) cc_final: 0.8193 (ttm) REVERT: T 359 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8524 (pt) REVERT: V 345 LYS cc_start: 0.8271 (mttt) cc_final: 0.8047 (tmtt) REVERT: V 353 LYS cc_start: 0.9067 (pttt) cc_final: 0.8854 (mmmt) REVERT: V 358 MET cc_start: 0.8783 (tpp) cc_final: 0.8299 (tpp) outliers start: 140 outliers final: 54 residues processed: 1115 average time/residue: 0.3754 time to fit residues: 619.8338 Evaluate side-chains 952 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 869 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 126 ILE Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 144 ASN Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 79 ASN Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 126 ILE Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 144 ASN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 126 ILE Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 144 ASN Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 79 ASN Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 126 ILE Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 144 ASN Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 126 ILE Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 144 ASN Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 79 ASN Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 126 ILE Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 144 ASN Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 126 ILE Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 144 ASN Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 79 ASN Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 144 ASN Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain U residue 360 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain H residue 359 LEU Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 359 LEU Chi-restraints excluded: chain V residue 359 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 79 ASN Y 41 GLN Y 79 ASN Z 79 ASN 0 41 GLN 0 79 ASN 2 41 GLN 8 79 ASN x 144 ASN y 144 ASN z 144 ASN 1 144 ASN ** 3 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 144 ASN 5 144 ASN ** 7 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 144 ASN 9 144 ASN J 351 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22224 Z= 0.219 Angle : 0.612 7.455 30080 Z= 0.326 Chirality : 0.045 0.165 3392 Planarity : 0.004 0.043 3744 Dihedral : 8.827 59.979 3070 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 6.54 % Allowed : 17.04 % Favored : 76.42 % 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: -2.80 (0.16), residues: 2624 helix: -0.36 (0.18), residues: 960 sheet: -1.90 (0.19), residues: 672 loop : -3.28 (0.15), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 364 HIS 0.002 0.001 HIS 9 137 PHE 0.017 0.001 PHE 5 150 TYR 0.017 0.001 TYR z 128 ARG 0.004 0.001 ARG X 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1018 time to evaluate : 2.562 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: X 65 GLN cc_start: 0.8290 (tt0) cc_final: 0.8085 (tt0) REVERT: X 70 ARG cc_start: 0.9021 (mtp85) cc_final: 0.8778 (mmm-85) REVERT: X 88 THR cc_start: 0.9494 (m) cc_final: 0.9236 (p) REVERT: X 117 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8107 (pp) REVERT: X 128 TYR cc_start: 0.9211 (t80) cc_final: 0.8981 (t80) REVERT: X 133 ASN cc_start: 0.8892 (m-40) cc_final: 0.8184 (t0) REVERT: X 144 ASN cc_start: 0.8644 (t0) cc_final: 0.8402 (t0) REVERT: Y 37 LYS cc_start: 0.9205 (tttt) cc_final: 0.8838 (ttmm) REVERT: Y 65 GLN cc_start: 0.8375 (tt0) cc_final: 0.7976 (tt0) REVERT: Y 70 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8623 (mmt90) REVERT: Y 85 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8105 (tm-30) REVERT: Y 88 THR cc_start: 0.9586 (m) cc_final: 0.9308 (p) REVERT: Y 97 LYS cc_start: 0.9102 (mtpp) cc_final: 0.8752 (tttp) REVERT: Y 133 ASN cc_start: 0.9011 (m-40) cc_final: 0.8686 (t0) REVERT: Y 138 ARG cc_start: 0.7919 (mtp85) cc_final: 0.7702 (mtp85) REVERT: Y 144 ASN cc_start: 0.8576 (t0) cc_final: 0.7580 (p0) REVERT: Z 65 GLN cc_start: 0.8280 (tt0) cc_final: 0.8073 (tt0) REVERT: Z 88 THR cc_start: 0.9518 (m) cc_final: 0.9227 (p) REVERT: Z 97 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8521 (tttm) REVERT: Z 117 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8103 (pp) REVERT: Z 128 TYR cc_start: 0.9209 (t80) cc_final: 0.8986 (t80) REVERT: Z 133 ASN cc_start: 0.8898 (m-40) cc_final: 0.8128 (t0) REVERT: Z 144 ASN cc_start: 0.8646 (t0) cc_final: 0.8407 (t0) REVERT: 0 65 GLN cc_start: 0.8285 (tt0) cc_final: 0.7957 (tt0) REVERT: 0 85 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8018 (tm-30) REVERT: 0 88 THR cc_start: 0.9593 (m) cc_final: 0.9272 (p) REVERT: 0 97 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8814 (tttp) REVERT: 0 133 ASN cc_start: 0.9023 (m-40) cc_final: 0.8594 (t0) REVERT: 0 138 ARG cc_start: 0.7862 (mtp85) cc_final: 0.7586 (mtp85) REVERT: 0 144 ASN cc_start: 0.8555 (t0) cc_final: 0.8318 (t0) REVERT: 2 65 GLN cc_start: 0.8377 (tt0) cc_final: 0.7962 (tt0) REVERT: 2 68 LYS cc_start: 0.9331 (mttt) cc_final: 0.9118 (mttp) REVERT: 2 70 ARG cc_start: 0.9073 (mtp85) cc_final: 0.8862 (mmm-85) REVERT: 2 88 THR cc_start: 0.9526 (m) cc_final: 0.9215 (p) REVERT: 2 97 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8539 (tttm) REVERT: 2 117 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8092 (pp) REVERT: 2 128 TYR cc_start: 0.9221 (t80) cc_final: 0.8996 (t80) REVERT: 2 133 ASN cc_start: 0.8913 (m-40) cc_final: 0.8179 (t0) REVERT: 2 144 ASN cc_start: 0.8651 (t0) cc_final: 0.8396 (t0) REVERT: 4 65 GLN cc_start: 0.8334 (tt0) cc_final: 0.8050 (tt0) REVERT: 4 85 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8083 (tm-30) REVERT: 4 88 THR cc_start: 0.9620 (m) cc_final: 0.9343 (p) REVERT: 4 97 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8852 (tttp) REVERT: 4 133 ASN cc_start: 0.9025 (m-40) cc_final: 0.8578 (t0) REVERT: 4 138 ARG cc_start: 0.7866 (mtp85) cc_final: 0.7580 (mtp85) REVERT: 4 144 ASN cc_start: 0.8602 (t0) cc_final: 0.8325 (t0) REVERT: 6 65 GLN cc_start: 0.8400 (tt0) cc_final: 0.7973 (tt0) REVERT: 6 88 THR cc_start: 0.9523 (m) cc_final: 0.9208 (p) REVERT: 6 97 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8536 (tttm) REVERT: 6 117 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7891 (pp) REVERT: 6 128 TYR cc_start: 0.9214 (t80) cc_final: 0.8997 (t80) REVERT: 6 133 ASN cc_start: 0.8909 (m-40) cc_final: 0.8120 (t0) REVERT: 6 144 ASN cc_start: 0.8634 (t0) cc_final: 0.8393 (t0) REVERT: 8 37 LYS cc_start: 0.8966 (tttt) cc_final: 0.8674 (tttp) REVERT: 8 65 GLN cc_start: 0.8395 (tt0) cc_final: 0.7954 (tt0) REVERT: 8 70 ARG cc_start: 0.8982 (mmt90) cc_final: 0.8743 (mmt90) REVERT: 8 85 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8041 (tm-30) REVERT: 8 88 THR cc_start: 0.9563 (m) cc_final: 0.9245 (p) REVERT: 8 97 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8741 (tttp) REVERT: 8 117 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7898 (pp) REVERT: 8 128 TYR cc_start: 0.9140 (t80) cc_final: 0.8930 (t80) REVERT: 8 133 ASN cc_start: 0.8962 (m-40) cc_final: 0.8620 (t0) REVERT: 8 138 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7749 (mtp85) REVERT: 8 144 ASN cc_start: 0.8591 (t0) cc_final: 0.7452 (p0) REVERT: x 37 LYS cc_start: 0.8907 (mttt) cc_final: 0.8616 (ttmt) REVERT: x 65 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8599 (tm-30) REVERT: x 74 GLU cc_start: 0.7557 (tt0) cc_final: 0.7253 (tt0) REVERT: x 81 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7706 (tm-30) REVERT: x 82 GLU cc_start: 0.8340 (mp0) cc_final: 0.7754 (mp0) REVERT: x 86 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8613 (ttpp) REVERT: x 97 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8390 (tttp) REVERT: x 117 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8011 (pp) REVERT: y 52 PHE cc_start: 0.8991 (t80) cc_final: 0.8645 (t80) REVERT: y 58 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.6429 (m-10) REVERT: y 65 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8507 (tm-30) REVERT: y 85 GLU cc_start: 0.8134 (tp30) cc_final: 0.7764 (tm-30) REVERT: y 86 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8470 (ttpp) REVERT: y 97 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8497 (tttm) REVERT: y 109 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7890 (mt-10) REVERT: y 117 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8091 (pp) REVERT: z 37 LYS cc_start: 0.8772 (mttt) cc_final: 0.8554 (ttmt) REVERT: z 65 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8532 (tm-30) REVERT: z 74 GLU cc_start: 0.7675 (tt0) cc_final: 0.7193 (tt0) REVERT: z 85 GLU cc_start: 0.8101 (tp30) cc_final: 0.7682 (tm-30) REVERT: z 86 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8739 (mmtm) REVERT: z 97 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8300 (tttp) REVERT: z 117 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8270 (pp) REVERT: z 138 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8040 (mtm-85) REVERT: z 171 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7224 (pmtt) REVERT: 1 52 PHE cc_start: 0.9022 (t80) cc_final: 0.8620 (t80) REVERT: 1 58 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6447 (m-10) REVERT: 1 65 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8573 (tm-30) REVERT: 1 85 GLU cc_start: 0.8128 (tp30) cc_final: 0.7743 (tm-30) REVERT: 1 86 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8389 (mtpt) REVERT: 1 97 LYS cc_start: 0.9154 (ttmt) cc_final: 0.8537 (tttm) REVERT: 1 117 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8071 (pp) REVERT: 3 86 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8526 (ttpp) REVERT: 3 97 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8372 (tttp) REVERT: 3 117 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8027 (pp) REVERT: 5 52 PHE cc_start: 0.8998 (t80) cc_final: 0.8629 (t80) REVERT: 5 58 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: 5 65 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8567 (tm-30) REVERT: 5 85 GLU cc_start: 0.8131 (tp30) cc_final: 0.7752 (tm-30) REVERT: 5 86 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8656 (mtpt) REVERT: 5 97 LYS cc_start: 0.9158 (ttmt) cc_final: 0.8530 (tttm) REVERT: 5 117 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8087 (pp) REVERT: 5 127 GLN cc_start: 0.8989 (tp40) cc_final: 0.8719 (tp40) REVERT: 5 128 TYR cc_start: 0.9181 (t80) cc_final: 0.8973 (t80) REVERT: 5 171 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7116 (pmtt) REVERT: 7 37 LYS cc_start: 0.8928 (mttt) cc_final: 0.8597 (ttmt) REVERT: 7 74 GLU cc_start: 0.7702 (tt0) cc_final: 0.7246 (tt0) REVERT: 7 86 LYS cc_start: 0.9247 (ttpt) cc_final: 0.8575 (ttpp) REVERT: 7 97 LYS cc_start: 0.9228 (ttpt) cc_final: 0.8521 (tttp) REVERT: 7 109 GLU cc_start: 0.8269 (mp0) cc_final: 0.7890 (mt-10) REVERT: 7 117 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8058 (pp) REVERT: 7 171 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6978 (pmtt) REVERT: 9 52 PHE cc_start: 0.8994 (t80) cc_final: 0.8632 (t80) REVERT: 9 58 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6379 (m-10) REVERT: 9 65 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8492 (tm-30) REVERT: 9 85 GLU cc_start: 0.8129 (tp30) cc_final: 0.7766 (tm-30) REVERT: 9 86 LYS cc_start: 0.8940 (ttpt) cc_final: 0.8406 (ttpp) REVERT: 9 97 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8427 (tttm) REVERT: 9 109 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7877 (mt-10) REVERT: 9 117 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8102 (pp) REVERT: 9 171 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7146 (pmtt) REVERT: A 345 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8180 (mmmt) REVERT: A 354 ASP cc_start: 0.7940 (m-30) cc_final: 0.7580 (m-30) REVERT: A 359 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7384 (pp) REVERT: D 354 ASP cc_start: 0.8005 (m-30) cc_final: 0.7719 (m-30) REVERT: D 358 MET cc_start: 0.7965 (tpp) cc_final: 0.7650 (tpp) REVERT: D 359 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (pp) REVERT: G 345 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8235 (mmmt) REVERT: G 359 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7287 (pp) REVERT: J 342 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.7972 (p0) REVERT: J 354 ASP cc_start: 0.8123 (m-30) cc_final: 0.7916 (m-30) REVERT: J 358 MET cc_start: 0.7992 (tpp) cc_final: 0.7748 (tpp) REVERT: M 345 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8359 (mmmt) REVERT: M 359 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7317 (pp) REVERT: P 354 ASP cc_start: 0.7951 (m-30) cc_final: 0.7176 (m-30) REVERT: P 356 TYR cc_start: 0.9369 (p90) cc_final: 0.9151 (p90) REVERT: S 359 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7275 (pp) REVERT: U 354 ASP cc_start: 0.8046 (m-30) cc_final: 0.7575 (m-30) REVERT: U 358 MET cc_start: 0.8042 (tpp) cc_final: 0.7681 (tpp) REVERT: U 359 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7628 (pp) REVERT: B 343 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7865 (p0) REVERT: E 345 LYS cc_start: 0.8253 (mttt) cc_final: 0.7987 (tmtt) REVERT: H 358 MET cc_start: 0.8525 (tpp) cc_final: 0.8309 (tpp) REVERT: K 339 LEU cc_start: 0.8992 (mt) cc_final: 0.8558 (tt) REVERT: K 345 LYS cc_start: 0.8263 (mttt) cc_final: 0.8038 (tmtt) REVERT: K 353 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8755 (mttt) REVERT: K 365 PHE cc_start: 0.8942 (t80) cc_final: 0.8694 (t80) REVERT: N 358 MET cc_start: 0.8433 (tpp) cc_final: 0.8232 (tpp) REVERT: Q 353 LYS cc_start: 0.9092 (pttt) cc_final: 0.8618 (mmmt) REVERT: Q 358 MET cc_start: 0.8605 (tpp) cc_final: 0.8300 (tpp) REVERT: T 358 MET cc_start: 0.8515 (tpp) cc_final: 0.8266 (tpp) REVERT: V 353 LYS cc_start: 0.9058 (pttt) cc_final: 0.8723 (mmmt) REVERT: V 358 MET cc_start: 0.8702 (tpp) cc_final: 0.8408 (tpp) outliers start: 157 outliers final: 68 residues processed: 1092 average time/residue: 0.3680 time to fit residues: 589.4927 Evaluate side-chains 1040 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 942 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 119 ASN Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 119 ASN Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 119 ASN Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 119 ASN Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 126 ILE Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 126 ILE Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 126 ILE Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 126 ILE Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 126 ILE Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 126 ILE Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 5 residue 171 LYS Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 126 ILE Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 171 LYS Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 126 ILE Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 LYS Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 359 LEU Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 359 LEU Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 79 ASN J 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22224 Z= 0.348 Angle : 0.668 8.011 30080 Z= 0.354 Chirality : 0.046 0.184 3392 Planarity : 0.004 0.041 3744 Dihedral : 8.271 57.122 3036 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 7.96 % Allowed : 19.21 % Favored : 72.83 % 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: -2.39 (0.16), residues: 2624 helix: -0.25 (0.18), residues: 976 sheet: -1.20 (0.21), residues: 640 loop : -3.20 (0.15), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 364 HIS 0.004 0.001 HIS Y 137 PHE 0.019 0.002 PHE 2 48 TYR 0.018 0.002 TYR J 349 ARG 0.005 0.001 ARG 7 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 917 time to evaluate : 2.809 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: X 65 GLN cc_start: 0.8367 (tt0) cc_final: 0.8117 (tt0) REVERT: X 68 LYS cc_start: 0.9223 (mttp) cc_final: 0.9019 (mttp) REVERT: X 70 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8858 (mmm-85) REVERT: X 79 ASN cc_start: 0.9080 (p0) cc_final: 0.8825 (p0) REVERT: X 81 GLU cc_start: 0.8544 (pm20) cc_final: 0.8314 (pm20) REVERT: X 88 THR cc_start: 0.9534 (m) cc_final: 0.9253 (p) REVERT: X 97 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8658 (tttm) REVERT: X 117 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8078 (pp) REVERT: X 133 ASN cc_start: 0.8932 (m-40) cc_final: 0.8282 (t0) REVERT: Y 37 LYS cc_start: 0.9181 (mttt) cc_final: 0.8733 (ttmm) REVERT: Y 48 PHE cc_start: 0.8959 (t80) cc_final: 0.8720 (t80) REVERT: Y 65 GLN cc_start: 0.8433 (tt0) cc_final: 0.8052 (tt0) REVERT: Y 85 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8142 (tm-30) REVERT: Y 88 THR cc_start: 0.9602 (m) cc_final: 0.9262 (p) REVERT: Y 117 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8090 (pp) REVERT: Y 133 ASN cc_start: 0.8955 (m-40) cc_final: 0.8548 (t0) REVERT: Y 136 ASP cc_start: 0.8011 (p0) cc_final: 0.7728 (p0) REVERT: Z 65 GLN cc_start: 0.8341 (tt0) cc_final: 0.8122 (tt0) REVERT: Z 79 ASN cc_start: 0.9096 (p0) cc_final: 0.8832 (p0) REVERT: Z 81 GLU cc_start: 0.8554 (pm20) cc_final: 0.8325 (pm20) REVERT: Z 85 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8306 (tm-30) REVERT: Z 88 THR cc_start: 0.9536 (m) cc_final: 0.9227 (p) REVERT: Z 97 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8666 (tttm) REVERT: Z 117 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8072 (pp) REVERT: Z 133 ASN cc_start: 0.8937 (m-40) cc_final: 0.8269 (t0) REVERT: 0 37 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.7548 (tptm) REVERT: 0 48 PHE cc_start: 0.8973 (t80) cc_final: 0.8746 (t80) REVERT: 0 65 GLN cc_start: 0.8343 (tt0) cc_final: 0.8068 (tt0) REVERT: 0 85 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8159 (tm-30) REVERT: 0 88 THR cc_start: 0.9608 (m) cc_final: 0.9315 (p) REVERT: 0 117 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7953 (pp) REVERT: 0 133 ASN cc_start: 0.8990 (m-40) cc_final: 0.8583 (t0) REVERT: 0 165 THR cc_start: 0.9463 (m) cc_final: 0.9160 (t) REVERT: 2 65 GLN cc_start: 0.8317 (tt0) cc_final: 0.7876 (tt0) REVERT: 2 68 LYS cc_start: 0.9267 (mttt) cc_final: 0.8912 (mttp) REVERT: 2 70 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8863 (mmm-85) REVERT: 2 81 GLU cc_start: 0.8616 (pm20) cc_final: 0.8340 (pm20) REVERT: 2 85 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8093 (tm-30) REVERT: 2 88 THR cc_start: 0.9525 (m) cc_final: 0.9242 (p) REVERT: 2 97 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8674 (tttm) REVERT: 2 117 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8064 (pp) REVERT: 2 133 ASN cc_start: 0.8939 (m-40) cc_final: 0.8266 (t0) REVERT: 4 37 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.7567 (tptm) REVERT: 4 48 PHE cc_start: 0.8933 (t80) cc_final: 0.8651 (t80) REVERT: 4 65 GLN cc_start: 0.8357 (tt0) cc_final: 0.8015 (tt0) REVERT: 4 81 GLU cc_start: 0.8453 (pm20) cc_final: 0.7935 (pm20) REVERT: 4 85 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8113 (tm-30) REVERT: 4 88 THR cc_start: 0.9606 (m) cc_final: 0.9317 (p) REVERT: 4 133 ASN cc_start: 0.8961 (m-40) cc_final: 0.8510 (t0) REVERT: 4 144 ASN cc_start: 0.8524 (t0) cc_final: 0.8279 (t0) REVERT: 6 65 GLN cc_start: 0.8376 (tt0) cc_final: 0.8117 (tt0) REVERT: 6 81 GLU cc_start: 0.8613 (pm20) cc_final: 0.8342 (pm20) REVERT: 6 85 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8087 (tm-30) REVERT: 6 88 THR cc_start: 0.9543 (m) cc_final: 0.9248 (p) REVERT: 6 97 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8677 (tttm) REVERT: 6 117 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8085 (pp) REVERT: 6 133 ASN cc_start: 0.8943 (m-40) cc_final: 0.8264 (t0) REVERT: 8 37 LYS cc_start: 0.9000 (mttt) cc_final: 0.8717 (ttmm) REVERT: 8 65 GLN cc_start: 0.8424 (tt0) cc_final: 0.8068 (tt0) REVERT: 8 70 ARG cc_start: 0.9005 (mmt90) cc_final: 0.8777 (mmt90) REVERT: 8 85 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8166 (tm-30) REVERT: 8 88 THR cc_start: 0.9568 (m) cc_final: 0.9225 (p) REVERT: 8 117 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7900 (pp) REVERT: 8 133 ASN cc_start: 0.8944 (m-40) cc_final: 0.8554 (t0) REVERT: 8 136 ASP cc_start: 0.8018 (p0) cc_final: 0.7744 (p0) REVERT: x 48 PHE cc_start: 0.8906 (t80) cc_final: 0.8359 (t80) REVERT: x 65 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8249 (tm-30) REVERT: x 70 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8527 (mtt-85) REVERT: x 74 GLU cc_start: 0.7533 (tt0) cc_final: 0.7182 (tt0) REVERT: x 86 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8460 (ttpp) REVERT: x 97 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8359 (tttp) REVERT: x 102 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8164 (tp) REVERT: x 109 GLU cc_start: 0.8160 (mp0) cc_final: 0.7864 (mp0) REVERT: x 117 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8025 (pp) REVERT: y 58 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: y 65 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8585 (tm-30) REVERT: y 85 GLU cc_start: 0.8286 (tp30) cc_final: 0.7831 (tm-30) REVERT: y 86 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8253 (ttpp) REVERT: y 97 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8554 (tttm) REVERT: y 109 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7738 (mt-10) REVERT: y 117 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8037 (pp) REVERT: y 144 ASN cc_start: 0.8599 (t0) cc_final: 0.8364 (m-40) REVERT: z 52 PHE cc_start: 0.9143 (t80) cc_final: 0.8883 (t80) REVERT: z 65 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8593 (tm-30) REVERT: z 74 GLU cc_start: 0.7706 (tt0) cc_final: 0.7389 (tt0) REVERT: z 82 GLU cc_start: 0.8373 (mp0) cc_final: 0.7852 (mp0) REVERT: z 86 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8539 (ttpp) REVERT: z 97 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8414 (tttp) REVERT: z 102 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8143 (tp) REVERT: z 117 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8054 (pp) REVERT: z 138 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8307 (mtm-85) REVERT: z 171 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7306 (pmtt) REVERT: 1 58 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6556 (m-10) REVERT: 1 65 GLN cc_start: 0.9326 (tm-30) cc_final: 0.8538 (tm-30) REVERT: 1 85 GLU cc_start: 0.8300 (tp30) cc_final: 0.7814 (tm-30) REVERT: 1 86 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8291 (ttpp) REVERT: 1 97 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8569 (tttm) REVERT: 1 117 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.7994 (pp) REVERT: 1 144 ASN cc_start: 0.8608 (t0) cc_final: 0.8373 (m-40) REVERT: 3 37 LYS cc_start: 0.8942 (mttt) cc_final: 0.8644 (tttt) REVERT: 3 65 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8559 (tm-30) REVERT: 3 70 ARG cc_start: 0.8764 (mtt-85) cc_final: 0.8535 (mtt-85) REVERT: 3 86 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8474 (ttpp) REVERT: 3 97 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8361 (tttp) REVERT: 3 117 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7984 (pp) REVERT: 5 58 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6559 (m-10) REVERT: 5 65 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8540 (tm-30) REVERT: 5 85 GLU cc_start: 0.8294 (tp30) cc_final: 0.7807 (tm-30) REVERT: 5 86 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8511 (ttpp) REVERT: 5 97 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8561 (tttm) REVERT: 5 117 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8028 (pp) REVERT: 5 127 GLN cc_start: 0.9035 (tp40) cc_final: 0.8779 (tp40) REVERT: 5 144 ASN cc_start: 0.8610 (t0) cc_final: 0.8373 (m-40) REVERT: 7 37 LYS cc_start: 0.8960 (mttt) cc_final: 0.8659 (tttt) REVERT: 7 65 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8792 (tm-30) REVERT: 7 70 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.8554 (mtt-85) REVERT: 7 74 GLU cc_start: 0.7628 (tt0) cc_final: 0.6973 (tt0) REVERT: 7 86 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8505 (ttpp) REVERT: 7 97 LYS cc_start: 0.9253 (ttpt) cc_final: 0.8608 (tttp) REVERT: 7 102 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8134 (tp) REVERT: 7 109 GLU cc_start: 0.8312 (mp0) cc_final: 0.7863 (mp0) REVERT: 7 117 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8016 (pp) REVERT: 9 58 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6591 (m-10) REVERT: 9 65 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8568 (tm-30) REVERT: 9 85 GLU cc_start: 0.8285 (tp30) cc_final: 0.7830 (tm-30) REVERT: 9 86 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8259 (ttpp) REVERT: 9 97 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8519 (tttm) REVERT: 9 109 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7845 (mt-10) REVERT: 9 117 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8038 (pp) REVERT: 9 144 ASN cc_start: 0.8593 (t0) cc_final: 0.8364 (m-40) REVERT: 9 171 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7598 (pmtt) REVERT: A 345 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8349 (mmmt) REVERT: A 354 ASP cc_start: 0.8084 (m-30) cc_final: 0.7685 (m-30) REVERT: A 359 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7216 (pp) REVERT: D 354 ASP cc_start: 0.8269 (m-30) cc_final: 0.7958 (m-30) REVERT: D 358 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7675 (tpp) REVERT: D 359 LEU cc_start: 0.8017 (pp) cc_final: 0.7640 (pp) REVERT: G 345 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8349 (mmmt) REVERT: G 359 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7203 (pp) REVERT: J 354 ASP cc_start: 0.8324 (m-30) cc_final: 0.8018 (m-30) REVERT: J 358 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7775 (tpp) REVERT: M 345 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8450 (mmmt) REVERT: M 359 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7425 (pp) REVERT: P 342 ASP cc_start: 0.8709 (p0) cc_final: 0.8303 (p0) REVERT: P 345 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8309 (tppt) REVERT: P 354 ASP cc_start: 0.8031 (m-30) cc_final: 0.7371 (m-30) REVERT: S 345 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8385 (mmmt) REVERT: S 354 ASP cc_start: 0.8010 (m-30) cc_final: 0.7682 (m-30) REVERT: S 359 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7390 (pp) REVERT: U 354 ASP cc_start: 0.8141 (m-30) cc_final: 0.7561 (m-30) REVERT: U 358 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7665 (tpp) REVERT: U 359 LEU cc_start: 0.7996 (pp) cc_final: 0.7611 (pp) REVERT: H 358 MET cc_start: 0.8474 (tpp) cc_final: 0.8099 (tpp) REVERT: K 365 PHE cc_start: 0.8891 (t80) cc_final: 0.8668 (t80) REVERT: N 358 MET cc_start: 0.8542 (tpp) cc_final: 0.8096 (tpp) REVERT: Q 353 LYS cc_start: 0.9126 (pttt) cc_final: 0.8657 (mmmt) REVERT: Q 358 MET cc_start: 0.8659 (tpp) cc_final: 0.8290 (tpp) REVERT: T 358 MET cc_start: 0.8510 (tpp) cc_final: 0.8101 (tpp) REVERT: V 343 ASP cc_start: 0.8148 (p0) cc_final: 0.7915 (p0) REVERT: V 353 LYS cc_start: 0.9096 (pttt) cc_final: 0.8664 (mmmt) REVERT: V 358 MET cc_start: 0.8733 (tpp) cc_final: 0.8342 (tpp) outliers start: 191 outliers final: 125 residues processed: 1016 average time/residue: 0.3774 time to fit residues: 560.0401 Evaluate side-chains 1049 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 891 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 119 ASN Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain X residue 171 LYS Chi-restraints excluded: chain Y residue 43 ASP Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 160 GLU Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 43 ASP Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 119 ASN Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain Z residue 171 LYS Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 43 ASP Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 0 residue 160 GLU Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 43 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 119 ASN Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 2 residue 171 LYS Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 43 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 120 ILE Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 160 GLU Chi-restraints excluded: chain 6 residue 43 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 119 ASN Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 6 residue 171 LYS Chi-restraints excluded: chain 8 residue 43 ASP Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain 8 residue 160 GLU Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 47 SER Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 112 SER Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 160 GLU Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 43 ASP Chi-restraints excluded: chain 1 residue 47 SER Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 112 SER Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 160 GLU Chi-restraints excluded: chain 1 residue 165 THR Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 160 GLU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 5 residue 43 ASP Chi-restraints excluded: chain 5 residue 47 SER Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 112 SER Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 165 THR Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 102 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 9 residue 43 ASP Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 112 SER Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 165 THR Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain P residue 359 LEU Chi-restraints excluded: chain S residue 359 LEU Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 359 LEU Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 233 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 79 ASN 8 79 ASN J 360 ASN P 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22224 Z= 0.208 Angle : 0.608 7.696 30080 Z= 0.324 Chirality : 0.045 0.156 3392 Planarity : 0.004 0.036 3744 Dihedral : 7.858 59.161 3016 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 6.29 % Allowed : 23.04 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2624 helix: 0.04 (0.18), residues: 976 sheet: -0.79 (0.21), residues: 640 loop : -3.05 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 364 HIS 0.002 0.000 HIS 0 137 PHE 0.019 0.002 PHE 9 48 TYR 0.017 0.001 TYR P 349 ARG 0.009 0.001 ARG 4 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 947 time to evaluate : 2.735 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: X 70 ARG cc_start: 0.9064 (mtp85) cc_final: 0.8835 (mmm-85) REVERT: X 81 GLU cc_start: 0.8625 (pm20) cc_final: 0.8400 (pm20) REVERT: X 85 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8254 (tm-30) REVERT: X 88 THR cc_start: 0.9509 (m) cc_final: 0.9178 (p) REVERT: X 97 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8601 (tttm) REVERT: X 117 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7796 (pp) REVERT: X 133 ASN cc_start: 0.8887 (m-40) cc_final: 0.8360 (t0) REVERT: X 144 ASN cc_start: 0.8609 (t0) cc_final: 0.8331 (t0) REVERT: Y 37 LYS cc_start: 0.9166 (mttt) cc_final: 0.8760 (ttmm) REVERT: Y 65 GLN cc_start: 0.8447 (tt0) cc_final: 0.8164 (tt0) REVERT: Y 70 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8531 (mmt90) REVERT: Y 85 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8142 (tm-30) REVERT: Y 88 THR cc_start: 0.9571 (m) cc_final: 0.9243 (p) REVERT: Y 133 ASN cc_start: 0.8919 (m-40) cc_final: 0.8566 (t0) REVERT: Y 144 ASN cc_start: 0.8205 (t0) cc_final: 0.7509 (p0) REVERT: Y 151 TYR cc_start: 0.8875 (t80) cc_final: 0.8655 (t80) REVERT: Z 81 GLU cc_start: 0.8625 (pm20) cc_final: 0.8408 (pm20) REVERT: Z 85 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8272 (tm-30) REVERT: Z 88 THR cc_start: 0.9506 (m) cc_final: 0.9163 (p) REVERT: Z 97 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8602 (tttm) REVERT: Z 117 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7797 (pp) REVERT: Z 133 ASN cc_start: 0.8895 (m-40) cc_final: 0.8371 (t0) REVERT: 0 85 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8130 (tm-30) REVERT: 0 88 THR cc_start: 0.9580 (m) cc_final: 0.9266 (p) REVERT: 0 133 ASN cc_start: 0.8935 (m-40) cc_final: 0.8544 (t0) REVERT: 0 144 ASN cc_start: 0.8208 (t0) cc_final: 0.7464 (p0) REVERT: 0 151 TYR cc_start: 0.8896 (t80) cc_final: 0.8658 (t80) REVERT: 2 65 GLN cc_start: 0.8224 (tt0) cc_final: 0.7782 (tt0) REVERT: 2 68 LYS cc_start: 0.9218 (mttt) cc_final: 0.8928 (mttp) REVERT: 2 70 ARG cc_start: 0.9057 (mtp85) cc_final: 0.8832 (mmm-85) REVERT: 2 85 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8062 (tm-30) REVERT: 2 88 THR cc_start: 0.9531 (m) cc_final: 0.9228 (p) REVERT: 2 97 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8614 (tttm) REVERT: 2 117 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7815 (pp) REVERT: 2 133 ASN cc_start: 0.8900 (m-40) cc_final: 0.8376 (t0) REVERT: 2 144 ASN cc_start: 0.8608 (t0) cc_final: 0.8361 (t0) REVERT: 4 37 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8956 (tptp) REVERT: 4 74 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7426 (tm-30) REVERT: 4 85 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8078 (tm-30) REVERT: 4 88 THR cc_start: 0.9574 (m) cc_final: 0.9271 (p) REVERT: 4 133 ASN cc_start: 0.8939 (m-40) cc_final: 0.8540 (t0) REVERT: 4 151 TYR cc_start: 0.8899 (t80) cc_final: 0.8683 (t80) REVERT: 6 65 GLN cc_start: 0.8205 (tt0) cc_final: 0.7805 (tt0) REVERT: 6 85 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8058 (tm-30) REVERT: 6 88 THR cc_start: 0.9530 (m) cc_final: 0.9227 (p) REVERT: 6 97 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8597 (tttm) REVERT: 6 117 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7841 (pp) REVERT: 6 133 ASN cc_start: 0.8899 (m-40) cc_final: 0.8370 (t0) REVERT: 6 144 ASN cc_start: 0.8594 (t0) cc_final: 0.8348 (t0) REVERT: 8 65 GLN cc_start: 0.8446 (tt0) cc_final: 0.8168 (tt0) REVERT: 8 74 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6974 (tm-30) REVERT: 8 85 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8101 (tm-30) REVERT: 8 88 THR cc_start: 0.9554 (m) cc_final: 0.9200 (p) REVERT: 8 117 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7636 (pp) REVERT: 8 133 ASN cc_start: 0.8904 (m-40) cc_final: 0.8555 (t0) REVERT: 8 144 ASN cc_start: 0.8271 (t0) cc_final: 0.7575 (p0) REVERT: x 37 LYS cc_start: 0.8858 (tttt) cc_final: 0.8504 (ttmt) REVERT: x 65 GLN cc_start: 0.9249 (tm-30) cc_final: 0.7937 (tm-30) REVERT: x 70 ARG cc_start: 0.8756 (mtt-85) cc_final: 0.8551 (mtt-85) REVERT: x 74 GLU cc_start: 0.7511 (tt0) cc_final: 0.7297 (tt0) REVERT: x 86 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8189 (ttpp) REVERT: x 97 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8205 (tttp) REVERT: x 109 GLU cc_start: 0.8213 (mp0) cc_final: 0.7717 (mp0) REVERT: x 117 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7744 (pp) REVERT: y 58 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6466 (m-10) REVERT: y 65 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8510 (tm-30) REVERT: y 85 GLU cc_start: 0.8191 (tp30) cc_final: 0.7752 (tm-30) REVERT: y 86 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8175 (ttpp) REVERT: y 97 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8486 (tttp) REVERT: y 109 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7647 (mt-10) REVERT: z 37 LYS cc_start: 0.8937 (tttt) cc_final: 0.8632 (ttmt) REVERT: z 65 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8297 (tm-30) REVERT: z 74 GLU cc_start: 0.7666 (tt0) cc_final: 0.7444 (tt0) REVERT: z 86 LYS cc_start: 0.8907 (ttpt) cc_final: 0.8254 (ttpp) REVERT: z 97 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8372 (tttp) REVERT: z 109 GLU cc_start: 0.8112 (mp0) cc_final: 0.7753 (mp0) REVERT: z 171 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7036 (pmtt) REVERT: 1 58 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6456 (m-10) REVERT: 1 65 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9019 (tm-30) REVERT: 1 85 GLU cc_start: 0.8240 (tp30) cc_final: 0.7775 (tm-30) REVERT: 1 86 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8436 (mtpt) REVERT: 1 97 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8524 (tttp) REVERT: 3 37 LYS cc_start: 0.8946 (mttt) cc_final: 0.8585 (ttmt) REVERT: 3 65 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8802 (tm-30) REVERT: 3 70 ARG cc_start: 0.8797 (mtt-85) cc_final: 0.8557 (mtt-85) REVERT: 3 86 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8026 (ttpp) REVERT: 3 97 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8341 (tttp) REVERT: 3 102 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8053 (tp) REVERT: 3 109 GLU cc_start: 0.8281 (mp0) cc_final: 0.8075 (mp0) REVERT: 3 147 ASP cc_start: 0.8230 (t0) cc_final: 0.7975 (m-30) REVERT: 5 58 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6476 (m-10) REVERT: 5 65 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9029 (tm-30) REVERT: 5 85 GLU cc_start: 0.8226 (tp30) cc_final: 0.7753 (tm-30) REVERT: 5 86 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8480 (ttpp) REVERT: 5 97 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8514 (tttp) REVERT: 5 117 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7846 (pp) REVERT: 7 37 LYS cc_start: 0.8941 (mttt) cc_final: 0.8712 (tttt) REVERT: 7 65 GLN cc_start: 0.9125 (tm-30) cc_final: 0.8368 (tm-30) REVERT: 7 70 ARG cc_start: 0.8802 (mtt-85) cc_final: 0.8573 (mtt-85) REVERT: 7 74 GLU cc_start: 0.7638 (tt0) cc_final: 0.7203 (tt0) REVERT: 7 86 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8002 (ttpp) REVERT: 7 97 LYS cc_start: 0.9285 (ttpt) cc_final: 0.8597 (tttp) REVERT: 7 109 GLU cc_start: 0.8350 (mp0) cc_final: 0.7849 (mp0) REVERT: 7 139 TYR cc_start: 0.8205 (m-80) cc_final: 0.7911 (m-80) REVERT: 9 50 GLU cc_start: 0.8948 (tt0) cc_final: 0.8381 (tm-30) REVERT: 9 58 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6404 (m-10) REVERT: 9 65 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9030 (tm-30) REVERT: 9 85 GLU cc_start: 0.8149 (tp30) cc_final: 0.7734 (tm-30) REVERT: 9 86 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8197 (ttpp) REVERT: 9 97 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8460 (tttm) REVERT: 9 171 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7007 (pmtt) REVERT: A 345 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8370 (mmmt) REVERT: A 354 ASP cc_start: 0.7979 (m-30) cc_final: 0.7612 (m-30) REVERT: D 354 ASP cc_start: 0.8229 (m-30) cc_final: 0.7961 (m-30) REVERT: D 359 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7606 (pp) REVERT: G 345 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8391 (mmmt) REVERT: G 359 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (pp) REVERT: J 345 LYS cc_start: 0.7778 (tppt) cc_final: 0.7498 (tppt) REVERT: J 347 LYS cc_start: 0.9176 (mmtp) cc_final: 0.8949 (mmtt) REVERT: J 354 ASP cc_start: 0.8150 (m-30) cc_final: 0.7885 (m-30) REVERT: J 358 MET cc_start: 0.8243 (tpp) cc_final: 0.7922 (tpp) REVERT: M 345 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8425 (mmmt) REVERT: M 354 ASP cc_start: 0.7702 (m-30) cc_final: 0.7417 (m-30) REVERT: P 342 ASP cc_start: 0.8603 (p0) cc_final: 0.8233 (p0) REVERT: P 345 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8092 (tppt) REVERT: P 354 ASP cc_start: 0.8007 (m-30) cc_final: 0.7214 (m-30) REVERT: S 345 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8361 (mmmt) REVERT: S 354 ASP cc_start: 0.7961 (m-30) cc_final: 0.7708 (m-30) REVERT: U 342 ASP cc_start: 0.8634 (p0) cc_final: 0.8396 (p0) REVERT: U 345 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8161 (tppt) REVERT: U 354 ASP cc_start: 0.8024 (m-30) cc_final: 0.7697 (m-30) REVERT: U 359 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7567 (pp) REVERT: B 343 ASP cc_start: 0.7896 (p0) cc_final: 0.7691 (p0) REVERT: B 358 MET cc_start: 0.8589 (tpp) cc_final: 0.7977 (tpp) REVERT: E 341 ASP cc_start: 0.8099 (p0) cc_final: 0.7866 (p0) REVERT: E 353 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8362 (mmmt) REVERT: H 358 MET cc_start: 0.8425 (tpp) cc_final: 0.8142 (tpp) REVERT: N 358 MET cc_start: 0.8431 (tpp) cc_final: 0.8126 (tpp) REVERT: Q 353 LYS cc_start: 0.9057 (pttt) cc_final: 0.8668 (mmmt) REVERT: Q 358 MET cc_start: 0.8586 (tpp) cc_final: 0.8272 (tpp) REVERT: T 358 MET cc_start: 0.8407 (tpp) cc_final: 0.8083 (tpp) REVERT: V 343 ASP cc_start: 0.8163 (p0) cc_final: 0.7909 (p0) REVERT: V 353 LYS cc_start: 0.9098 (pttt) cc_final: 0.8584 (mmmt) outliers start: 151 outliers final: 89 residues processed: 1010 average time/residue: 0.3603 time to fit residues: 537.7339 Evaluate side-chains 1017 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 909 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 131 ASP Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Y residue 160 GLU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 131 ASP Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 131 ASP Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 43 ASP Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 120 ILE Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 131 ASP Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain 8 residue 160 GLU Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 131 ASP Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 160 GLU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 131 ASP Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 131 ASP Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 131 ASP Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 160 GLU Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 343 ASP Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 359 LEU Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 343 ASP Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 359 LEU Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN J 360 ASN ** P 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22224 Z= 0.187 Angle : 0.606 8.064 30080 Z= 0.323 Chirality : 0.044 0.154 3392 Planarity : 0.004 0.036 3744 Dihedral : 7.611 59.665 3002 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 6.00 % Allowed : 24.92 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2624 helix: 0.32 (0.18), residues: 976 sheet: -0.45 (0.21), residues: 640 loop : -2.98 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 364 HIS 0.001 0.000 HIS 8 137 PHE 0.020 0.002 PHE 6 48 TYR 0.019 0.001 TYR J 349 ARG 0.006 0.001 ARG 0 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 947 time to evaluate : 2.416 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: X 70 ARG cc_start: 0.9070 (mtp85) cc_final: 0.8863 (mmm-85) REVERT: X 85 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8233 (tm-30) REVERT: X 88 THR cc_start: 0.9445 (m) cc_final: 0.9157 (p) REVERT: X 117 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7794 (pp) REVERT: X 133 ASN cc_start: 0.8954 (m-40) cc_final: 0.8271 (t0) REVERT: X 144 ASN cc_start: 0.8582 (t0) cc_final: 0.7848 (p0) REVERT: Y 37 LYS cc_start: 0.9166 (mttt) cc_final: 0.8898 (ttmm) REVERT: Y 70 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8578 (mmt90) REVERT: Y 74 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7347 (tm-30) REVERT: Y 85 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Y 88 THR cc_start: 0.9581 (m) cc_final: 0.9236 (p) REVERT: Y 133 ASN cc_start: 0.8925 (m-40) cc_final: 0.8549 (t0) REVERT: Y 144 ASN cc_start: 0.8347 (t0) cc_final: 0.7373 (p0) REVERT: Z 50 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7843 (pp20) REVERT: Z 85 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8270 (tm-30) REVERT: Z 88 THR cc_start: 0.9440 (m) cc_final: 0.9143 (p) REVERT: Z 117 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7924 (pp) REVERT: Z 133 ASN cc_start: 0.8963 (m-40) cc_final: 0.8293 (t0) REVERT: 0 85 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8244 (tm-30) REVERT: 0 88 THR cc_start: 0.9567 (m) cc_final: 0.9217 (p) REVERT: 0 133 ASN cc_start: 0.8929 (m-40) cc_final: 0.8522 (t0) REVERT: 0 144 ASN cc_start: 0.8246 (t0) cc_final: 0.7184 (p0) REVERT: 2 65 GLN cc_start: 0.8071 (tt0) cc_final: 0.7726 (tm-30) REVERT: 2 85 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8083 (tm-30) REVERT: 2 88 THR cc_start: 0.9510 (m) cc_final: 0.9180 (p) REVERT: 2 117 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7769 (pp) REVERT: 2 133 ASN cc_start: 0.8971 (m-40) cc_final: 0.8314 (t0) REVERT: 2 144 ASN cc_start: 0.8584 (t0) cc_final: 0.7853 (p0) REVERT: 4 37 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8975 (tmtt) REVERT: 4 85 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8099 (tm-30) REVERT: 4 88 THR cc_start: 0.9563 (m) cc_final: 0.9213 (p) REVERT: 4 133 ASN cc_start: 0.8934 (m-40) cc_final: 0.8532 (t0) REVERT: 4 144 ASN cc_start: 0.8096 (t0) cc_final: 0.7243 (p0) REVERT: 6 65 GLN cc_start: 0.8134 (tt0) cc_final: 0.7835 (tm-30) REVERT: 6 85 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8073 (tm-30) REVERT: 6 88 THR cc_start: 0.9492 (m) cc_final: 0.9160 (p) REVERT: 6 117 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7847 (pp) REVERT: 6 133 ASN cc_start: 0.8967 (m-40) cc_final: 0.8287 (t0) REVERT: 6 144 ASN cc_start: 0.8576 (t0) cc_final: 0.7858 (p0) REVERT: 8 37 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8384 (tptp) REVERT: 8 85 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8203 (tm-30) REVERT: 8 88 THR cc_start: 0.9547 (m) cc_final: 0.9149 (p) REVERT: 8 117 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7564 (pp) REVERT: 8 133 ASN cc_start: 0.8913 (m-40) cc_final: 0.8439 (t0) REVERT: 8 144 ASN cc_start: 0.8356 (t0) cc_final: 0.7340 (p0) REVERT: x 37 LYS cc_start: 0.8926 (tttt) cc_final: 0.8652 (ttmt) REVERT: x 65 GLN cc_start: 0.9270 (tm-30) cc_final: 0.7927 (tm-30) REVERT: x 74 GLU cc_start: 0.7467 (tt0) cc_final: 0.7032 (tt0) REVERT: x 81 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7582 (tm-30) REVERT: x 82 GLU cc_start: 0.8499 (mp0) cc_final: 0.7925 (mp0) REVERT: x 86 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8094 (ttpp) REVERT: x 97 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8306 (tttp) REVERT: x 109 GLU cc_start: 0.8186 (mp0) cc_final: 0.7682 (mp0) REVERT: x 139 TYR cc_start: 0.8303 (m-80) cc_final: 0.8094 (m-80) REVERT: y 58 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6283 (m-10) REVERT: y 65 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9095 (tm-30) REVERT: y 85 GLU cc_start: 0.8108 (tp30) cc_final: 0.7693 (tm-30) REVERT: y 86 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8433 (mtpt) REVERT: y 97 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8443 (tttp) REVERT: y 138 ARG cc_start: 0.8425 (mtp85) cc_final: 0.8101 (mtm-85) REVERT: y 147 ASP cc_start: 0.8223 (t0) cc_final: 0.7821 (m-30) REVERT: z 37 LYS cc_start: 0.8851 (tttt) cc_final: 0.8591 (ttmt) REVERT: z 65 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8141 (tm-30) REVERT: z 74 GLU cc_start: 0.7703 (tt0) cc_final: 0.7348 (tt0) REVERT: z 79 ASN cc_start: 0.8526 (p0) cc_final: 0.8323 (p0) REVERT: z 82 GLU cc_start: 0.8260 (mp0) cc_final: 0.7006 (mp0) REVERT: z 86 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8184 (ttpp) REVERT: z 97 LYS cc_start: 0.9036 (ttpt) cc_final: 0.8312 (tttp) REVERT: z 109 GLU cc_start: 0.8203 (mp0) cc_final: 0.7797 (mp0) REVERT: z 171 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6890 (pmtt) REVERT: 1 58 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6275 (m-10) REVERT: 1 65 GLN cc_start: 0.9393 (tm-30) cc_final: 0.9052 (tm-30) REVERT: 1 85 GLU cc_start: 0.8243 (tp30) cc_final: 0.7684 (tm-30) REVERT: 1 86 LYS cc_start: 0.8857 (ttpt) cc_final: 0.8567 (mtpt) REVERT: 1 97 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8439 (tttp) REVERT: 1 147 ASP cc_start: 0.8241 (t0) cc_final: 0.7838 (m-30) REVERT: 3 65 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8529 (tm-30) REVERT: 3 70 ARG cc_start: 0.8790 (mtt-85) cc_final: 0.8551 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7484 (tm-30) REVERT: 3 82 GLU cc_start: 0.8584 (mp0) cc_final: 0.7986 (mp0) REVERT: 3 86 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8242 (ttpp) REVERT: 3 97 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8294 (tttp) REVERT: 3 102 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7974 (tp) REVERT: 3 109 GLU cc_start: 0.8269 (mp0) cc_final: 0.8016 (mp0) REVERT: 3 147 ASP cc_start: 0.8282 (t0) cc_final: 0.7865 (m-30) REVERT: 5 58 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.6290 (m-10) REVERT: 5 65 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9039 (tm-30) REVERT: 5 85 GLU cc_start: 0.8177 (tp30) cc_final: 0.7660 (tm-30) REVERT: 5 86 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8555 (mtpt) REVERT: 5 97 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8437 (tttp) REVERT: 5 147 ASP cc_start: 0.8251 (t0) cc_final: 0.7839 (m-30) REVERT: 7 65 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8394 (tm-30) REVERT: 7 81 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7448 (tm-30) REVERT: 7 82 GLU cc_start: 0.8478 (mp0) cc_final: 0.7961 (mp0) REVERT: 7 86 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8016 (ttpp) REVERT: 7 97 LYS cc_start: 0.9217 (ttpt) cc_final: 0.8468 (tttp) REVERT: 7 109 GLU cc_start: 0.8249 (mp0) cc_final: 0.7719 (mp0) REVERT: 7 138 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8048 (mtm-85) REVERT: 9 50 GLU cc_start: 0.8955 (tt0) cc_final: 0.8435 (tm-30) REVERT: 9 58 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6228 (m-10) REVERT: 9 65 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9058 (tm-30) REVERT: 9 85 GLU cc_start: 0.8079 (tp30) cc_final: 0.7677 (tm-30) REVERT: 9 86 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8405 (mtpt) REVERT: 9 97 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8481 (tttp) REVERT: 9 138 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8086 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8224 (t0) cc_final: 0.7839 (m-30) REVERT: 9 171 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6805 (pmtt) REVERT: A 345 LYS cc_start: 0.8711 (mmmt) cc_final: 0.8489 (mmmt) REVERT: A 354 ASP cc_start: 0.7988 (m-30) cc_final: 0.7641 (m-30) REVERT: D 359 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7579 (pp) REVERT: G 345 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8481 (mmmt) REVERT: J 358 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7960 (tpp) REVERT: M 345 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8484 (mmmt) REVERT: M 354 ASP cc_start: 0.7870 (m-30) cc_final: 0.7471 (m-30) REVERT: P 342 ASP cc_start: 0.8553 (p0) cc_final: 0.8249 (p0) REVERT: P 345 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8138 (tppt) REVERT: P 354 ASP cc_start: 0.7989 (m-30) cc_final: 0.7569 (m-30) REVERT: S 345 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8502 (mmmt) REVERT: S 354 ASP cc_start: 0.7894 (m-30) cc_final: 0.7618 (m-30) REVERT: U 342 ASP cc_start: 0.8618 (p0) cc_final: 0.8398 (p0) REVERT: U 345 LYS cc_start: 0.8398 (mmmt) cc_final: 0.8130 (tppt) REVERT: U 359 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7570 (pp) REVERT: B 343 ASP cc_start: 0.7844 (p0) cc_final: 0.7375 (p0) REVERT: B 358 MET cc_start: 0.8499 (tpp) cc_final: 0.8185 (tpp) REVERT: E 353 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8327 (mmmt) REVERT: H 343 ASP cc_start: 0.7984 (p0) cc_final: 0.7535 (p0) REVERT: H 358 MET cc_start: 0.8402 (tpp) cc_final: 0.8129 (tpp) REVERT: K 362 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8652 (mmtt) REVERT: N 358 MET cc_start: 0.8363 (tpp) cc_final: 0.8100 (tpp) REVERT: Q 343 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7756 (p0) REVERT: Q 353 LYS cc_start: 0.9035 (pttt) cc_final: 0.8584 (mmmt) REVERT: T 358 MET cc_start: 0.8375 (tpp) cc_final: 0.8114 (tpp) REVERT: V 343 ASP cc_start: 0.8231 (p0) cc_final: 0.7956 (p0) REVERT: V 353 LYS cc_start: 0.9056 (pttt) cc_final: 0.8490 (mmmt) REVERT: V 361 ASP cc_start: 0.8134 (t0) cc_final: 0.7912 (t0) outliers start: 144 outliers final: 89 residues processed: 1007 average time/residue: 0.3577 time to fit residues: 532.8721 Evaluate side-chains 1020 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 912 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 37 LYS Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 50 GLU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 160 GLU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 160 GLU Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 343 ASP Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 359 LEU Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 79 ASN X 127 GLN Z 79 ASN Z 127 GLN ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 127 GLN y 41 GLN 5 41 GLN 9 41 GLN D 360 ASN U 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22224 Z= 0.223 Angle : 0.645 8.328 30080 Z= 0.343 Chirality : 0.045 0.150 3392 Planarity : 0.004 0.035 3744 Dihedral : 7.181 59.911 2978 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.83 % Allowed : 25.58 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2624 helix: 0.34 (0.18), residues: 976 sheet: -0.29 (0.21), residues: 640 loop : -2.96 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 364 HIS 0.001 0.001 HIS T 363 PHE 0.022 0.002 PHE 2 48 TYR 0.020 0.001 TYR 0 151 ARG 0.006 0.001 ARG 8 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 939 time to evaluate : 2.567 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: X 70 ARG cc_start: 0.9047 (mtp85) cc_final: 0.8812 (mmm-85) REVERT: X 85 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8202 (tm-30) REVERT: X 88 THR cc_start: 0.9438 (m) cc_final: 0.9103 (p) REVERT: X 117 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7743 (pp) REVERT: X 133 ASN cc_start: 0.8860 (m-40) cc_final: 0.8295 (t0) REVERT: Y 74 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7486 (tm-30) REVERT: Y 85 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8182 (tm-30) REVERT: Y 88 THR cc_start: 0.9582 (m) cc_final: 0.9234 (p) REVERT: Y 133 ASN cc_start: 0.8924 (m-40) cc_final: 0.8469 (t0) REVERT: Z 85 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8296 (tm-30) REVERT: Z 88 THR cc_start: 0.9450 (m) cc_final: 0.9075 (p) REVERT: Z 117 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7734 (pp) REVERT: Z 133 ASN cc_start: 0.8955 (m-40) cc_final: 0.8382 (t0) REVERT: 0 85 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8198 (tm-30) REVERT: 0 88 THR cc_start: 0.9568 (m) cc_final: 0.9207 (p) REVERT: 0 90 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (mm) REVERT: 0 96 TYR cc_start: 0.8841 (t80) cc_final: 0.8527 (t80) REVERT: 0 133 ASN cc_start: 0.8946 (m-40) cc_final: 0.8458 (t0) REVERT: 2 37 LYS cc_start: 0.8818 (tttm) cc_final: 0.8384 (tptm) REVERT: 2 65 GLN cc_start: 0.8083 (tt0) cc_final: 0.7841 (tm-30) REVERT: 2 85 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8068 (tm-30) REVERT: 2 88 THR cc_start: 0.9477 (m) cc_final: 0.9195 (p) REVERT: 2 117 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7760 (pp) REVERT: 2 133 ASN cc_start: 0.8960 (m-40) cc_final: 0.8382 (t0) REVERT: 4 37 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9070 (tptp) REVERT: 4 74 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7229 (tm-30) REVERT: 4 85 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8155 (tm-30) REVERT: 4 88 THR cc_start: 0.9573 (m) cc_final: 0.9228 (p) REVERT: 4 90 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9120 (mm) REVERT: 4 96 TYR cc_start: 0.8883 (t80) cc_final: 0.8567 (t80) REVERT: 4 133 ASN cc_start: 0.8948 (m-40) cc_final: 0.8548 (t0) REVERT: 4 144 ASN cc_start: 0.8218 (t0) cc_final: 0.7122 (p0) REVERT: 6 65 GLN cc_start: 0.8133 (tt0) cc_final: 0.7850 (tm-30) REVERT: 6 85 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8120 (tm-30) REVERT: 6 88 THR cc_start: 0.9466 (m) cc_final: 0.9166 (p) REVERT: 6 117 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7811 (pp) REVERT: 6 133 ASN cc_start: 0.8957 (m-40) cc_final: 0.8372 (t0) REVERT: 8 85 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8201 (tm-30) REVERT: 8 88 THR cc_start: 0.9559 (m) cc_final: 0.9151 (p) REVERT: 8 117 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7778 (pp) REVERT: 8 133 ASN cc_start: 0.8923 (m-40) cc_final: 0.8444 (t0) REVERT: x 37 LYS cc_start: 0.8863 (tttt) cc_final: 0.8577 (ttmt) REVERT: x 65 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8449 (tm-30) REVERT: x 74 GLU cc_start: 0.7487 (tt0) cc_final: 0.7037 (tt0) REVERT: x 81 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7628 (tm-30) REVERT: x 82 GLU cc_start: 0.8582 (mp0) cc_final: 0.7946 (mp0) REVERT: x 86 LYS cc_start: 0.8416 (ttpt) cc_final: 0.8135 (ttpp) REVERT: x 97 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8267 (tttp) REVERT: x 102 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (tp) REVERT: x 109 GLU cc_start: 0.8095 (mp0) cc_final: 0.7797 (mp0) REVERT: x 138 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8047 (mtm-85) REVERT: y 58 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: y 65 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8787 (tm-30) REVERT: y 86 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8519 (ttpp) REVERT: y 97 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8422 (tttm) REVERT: y 147 ASP cc_start: 0.8275 (t0) cc_final: 0.7910 (m-30) REVERT: y 148 LYS cc_start: 0.9230 (mtpt) cc_final: 0.8777 (mtmt) REVERT: z 37 LYS cc_start: 0.8839 (tttt) cc_final: 0.8560 (ttmt) REVERT: z 52 PHE cc_start: 0.9131 (t80) cc_final: 0.8869 (t80) REVERT: z 65 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8722 (tm-30) REVERT: z 74 GLU cc_start: 0.7727 (tt0) cc_final: 0.7404 (tt0) REVERT: z 86 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8231 (ttpp) REVERT: z 97 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8282 (tttp) REVERT: z 109 GLU cc_start: 0.8215 (mp0) cc_final: 0.7852 (mp0) REVERT: z 147 ASP cc_start: 0.8224 (t0) cc_final: 0.7738 (m-30) REVERT: z 171 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7068 (pmtt) REVERT: 1 58 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: 1 65 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8802 (tm-30) REVERT: 1 85 GLU cc_start: 0.8116 (tp30) cc_final: 0.7717 (tm-30) REVERT: 1 86 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8573 (mtpt) REVERT: 1 97 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8425 (tttm) REVERT: 1 138 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8110 (mtm-85) REVERT: 1 147 ASP cc_start: 0.8261 (t0) cc_final: 0.7902 (m-30) REVERT: 1 148 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8872 (mtmt) REVERT: 3 65 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8291 (tm-30) REVERT: 3 70 ARG cc_start: 0.8825 (mtt-85) cc_final: 0.8610 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7508 (tm-30) REVERT: 3 82 GLU cc_start: 0.8524 (mp0) cc_final: 0.7930 (mp0) REVERT: 3 86 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8060 (ttpp) REVERT: 3 97 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8364 (tttp) REVERT: 3 102 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8039 (tp) REVERT: 3 109 GLU cc_start: 0.8239 (mp0) cc_final: 0.7989 (mp0) REVERT: 3 147 ASP cc_start: 0.8288 (t0) cc_final: 0.7885 (m-30) REVERT: 5 58 TYR cc_start: 0.6749 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: 5 65 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8800 (tm-30) REVERT: 5 85 GLU cc_start: 0.8185 (tp30) cc_final: 0.7876 (tm-30) REVERT: 5 86 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8557 (mtpt) REVERT: 5 97 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8433 (tttm) REVERT: 5 147 ASP cc_start: 0.8279 (t0) cc_final: 0.7904 (m-30) REVERT: 5 148 LYS cc_start: 0.9251 (mtpt) cc_final: 0.8875 (mtmt) REVERT: 7 65 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8064 (tm-30) REVERT: 7 81 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7495 (tm-30) REVERT: 7 82 GLU cc_start: 0.8494 (mp0) cc_final: 0.7889 (mp0) REVERT: 7 86 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8054 (ttpp) REVERT: 7 97 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8487 (tttp) REVERT: 7 109 GLU cc_start: 0.8072 (mp0) cc_final: 0.7404 (mp0) REVERT: 7 138 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8074 (mtm-85) REVERT: 9 50 GLU cc_start: 0.8957 (tt0) cc_final: 0.8434 (tm-30) REVERT: 9 58 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: 9 65 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8751 (tm-30) REVERT: 9 86 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8552 (ttpp) REVERT: 9 97 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8430 (tttm) REVERT: 9 138 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8097 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8350 (t0) cc_final: 0.7685 (m-30) REVERT: 9 148 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8808 (mtmt) REVERT: 9 171 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7003 (pmtt) REVERT: A 345 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8507 (mmmt) REVERT: A 354 ASP cc_start: 0.8009 (m-30) cc_final: 0.7624 (m-30) REVERT: D 354 ASP cc_start: 0.8113 (m-30) cc_final: 0.7701 (m-30) REVERT: D 359 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7582 (pp) REVERT: G 345 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8508 (mmmt) REVERT: J 354 ASP cc_start: 0.8135 (m-30) cc_final: 0.7633 (m-30) REVERT: J 358 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (tpp) REVERT: M 345 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8542 (mmmt) REVERT: M 354 ASP cc_start: 0.7980 (m-30) cc_final: 0.7524 (m-30) REVERT: M 359 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7519 (pp) REVERT: P 354 ASP cc_start: 0.8002 (m-30) cc_final: 0.7606 (m-30) REVERT: S 354 ASP cc_start: 0.8002 (m-30) cc_final: 0.7674 (m-30) REVERT: U 342 ASP cc_start: 0.8577 (p0) cc_final: 0.8362 (p0) REVERT: U 345 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8147 (tppt) REVERT: U 354 ASP cc_start: 0.7975 (m-30) cc_final: 0.7686 (m-30) REVERT: U 359 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7569 (pp) REVERT: B 343 ASP cc_start: 0.7876 (p0) cc_final: 0.7416 (p0) REVERT: B 358 MET cc_start: 0.8514 (tpp) cc_final: 0.8110 (tpp) REVERT: E 353 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8504 (mmmt) REVERT: H 343 ASP cc_start: 0.8048 (p0) cc_final: 0.7662 (p0) REVERT: H 358 MET cc_start: 0.8411 (tpp) cc_final: 0.8097 (tpp) REVERT: K 343 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7767 (p0) REVERT: N 358 MET cc_start: 0.8360 (tpp) cc_final: 0.8027 (tpp) REVERT: Q 343 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7769 (p0) REVERT: Q 353 LYS cc_start: 0.9087 (pttt) cc_final: 0.8659 (mmmt) REVERT: T 358 MET cc_start: 0.8356 (tpp) cc_final: 0.8044 (tpp) REVERT: V 343 ASP cc_start: 0.8299 (p0) cc_final: 0.8045 (p0) REVERT: V 353 LYS cc_start: 0.9085 (pttt) cc_final: 0.8493 (mmmt) outliers start: 164 outliers final: 113 residues processed: 1015 average time/residue: 0.3606 time to fit residues: 544.4503 Evaluate side-chains 1043 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 907 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 79 ASN Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 165 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 79 ASN Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain Z residue 165 THR Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 90 LEU Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 87 LEU Chi-restraints excluded: chain 4 residue 90 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 160 GLU Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 165 THR Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain 8 residue 160 GLU Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 131 ASP Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 90 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 112 SER Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 131 ASP Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 160 GLU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 112 SER Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 131 ASP Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 90 LEU Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 43 ASP Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 118 GLU Chi-restraints excluded: chain 9 residue 131 ASP Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain M residue 359 LEU Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 343 ASP Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 208 optimal weight: 0.0060 chunk 138 optimal weight: 0.9990 chunk 246 optimal weight: 0.0770 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 79 ASN Z 79 ASN ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 127 GLN y 41 GLN z 79 ASN 5 41 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 360 ASN ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22224 Z= 0.184 Angle : 0.660 8.712 30080 Z= 0.349 Chirality : 0.045 0.203 3392 Planarity : 0.004 0.042 3744 Dihedral : 7.123 59.773 2976 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 5.96 % Allowed : 27.58 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2624 helix: 0.36 (0.18), residues: 976 sheet: -0.44 (0.21), residues: 672 loop : -2.85 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 364 HIS 0.001 0.000 HIS H 363 PHE 0.021 0.001 PHE 2 48 TYR 0.022 0.001 TYR P 349 ARG 0.006 0.001 ARG 0 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 957 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 70 ARG cc_start: 0.9035 (mtp85) cc_final: 0.8815 (mmm-85) REVERT: X 85 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8227 (tm-30) REVERT: X 88 THR cc_start: 0.9413 (m) cc_final: 0.9093 (p) REVERT: X 133 ASN cc_start: 0.8857 (m-40) cc_final: 0.8366 (t0) REVERT: X 151 TYR cc_start: 0.8964 (t80) cc_final: 0.8607 (t80) REVERT: Y 85 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8219 (tm-30) REVERT: Y 88 THR cc_start: 0.9565 (m) cc_final: 0.9215 (p) REVERT: Y 111 ILE cc_start: 0.9108 (mt) cc_final: 0.8908 (tt) REVERT: Y 133 ASN cc_start: 0.8860 (m-40) cc_final: 0.8403 (t0) REVERT: Y 136 ASP cc_start: 0.8235 (p0) cc_final: 0.8021 (p0) REVERT: Z 85 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8279 (tm-30) REVERT: Z 88 THR cc_start: 0.9410 (m) cc_final: 0.9086 (p) REVERT: Z 133 ASN cc_start: 0.8960 (m-40) cc_final: 0.8533 (t0) REVERT: Z 151 TYR cc_start: 0.9003 (t80) cc_final: 0.8596 (t80) REVERT: 0 37 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8855 (tptp) REVERT: 0 50 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8184 (pp20) REVERT: 0 84 LEU cc_start: 0.9289 (tp) cc_final: 0.9058 (tp) REVERT: 0 85 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8297 (tm-30) REVERT: 0 88 THR cc_start: 0.9534 (m) cc_final: 0.9191 (p) REVERT: 0 133 ASN cc_start: 0.8919 (m-40) cc_final: 0.8433 (t0) REVERT: 0 136 ASP cc_start: 0.8273 (p0) cc_final: 0.8061 (p0) REVERT: 2 37 LYS cc_start: 0.9012 (tttm) cc_final: 0.8367 (tptm) REVERT: 2 65 GLN cc_start: 0.8059 (tt0) cc_final: 0.7826 (tm-30) REVERT: 2 85 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8092 (tm-30) REVERT: 2 88 THR cc_start: 0.9473 (m) cc_final: 0.9160 (p) REVERT: 2 133 ASN cc_start: 0.8971 (m-40) cc_final: 0.8539 (t0) REVERT: 2 151 TYR cc_start: 0.9007 (t80) cc_final: 0.8643 (t80) REVERT: 4 37 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8917 (tmtt) REVERT: 4 85 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8231 (tm-30) REVERT: 4 88 THR cc_start: 0.9542 (m) cc_final: 0.9201 (p) REVERT: 4 133 ASN cc_start: 0.8920 (m-40) cc_final: 0.8430 (t0) REVERT: 4 136 ASP cc_start: 0.8257 (p0) cc_final: 0.8054 (p0) REVERT: 4 144 ASN cc_start: 0.8221 (t0) cc_final: 0.7093 (p0) REVERT: 6 37 LYS cc_start: 0.8886 (tttm) cc_final: 0.8318 (mmmt) REVERT: 6 85 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8113 (tm-30) REVERT: 6 88 THR cc_start: 0.9448 (m) cc_final: 0.9137 (p) REVERT: 6 133 ASN cc_start: 0.8957 (m-40) cc_final: 0.8520 (t0) REVERT: 6 151 TYR cc_start: 0.8962 (t80) cc_final: 0.8607 (t80) REVERT: 8 37 LYS cc_start: 0.9127 (tptp) cc_final: 0.8289 (tptp) REVERT: 8 74 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6414 (tm-30) REVERT: 8 85 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8243 (tm-30) REVERT: 8 88 THR cc_start: 0.9533 (m) cc_final: 0.9213 (p) REVERT: 8 111 ILE cc_start: 0.9115 (mt) cc_final: 0.8905 (tt) REVERT: 8 117 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7651 (pp) REVERT: 8 133 ASN cc_start: 0.8899 (m-40) cc_final: 0.8421 (t0) REVERT: 8 136 ASP cc_start: 0.8302 (p0) cc_final: 0.8087 (p0) REVERT: x 37 LYS cc_start: 0.8862 (tttt) cc_final: 0.8557 (ttmt) REVERT: x 65 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8546 (tm-30) REVERT: x 74 GLU cc_start: 0.7566 (tt0) cc_final: 0.7144 (tt0) REVERT: x 81 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7528 (tm-30) REVERT: x 82 GLU cc_start: 0.8525 (mp0) cc_final: 0.7907 (mp0) REVERT: x 86 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8197 (ttpp) REVERT: x 97 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8375 (tttp) REVERT: x 102 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7858 (tp) REVERT: x 137 HIS cc_start: 0.7813 (p-80) cc_final: 0.7598 (p-80) REVERT: x 138 ARG cc_start: 0.8508 (mtp85) cc_final: 0.7991 (mtm-85) REVERT: x 147 ASP cc_start: 0.8138 (t0) cc_final: 0.7741 (m-30) REVERT: y 58 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6239 (m-10) REVERT: y 65 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8761 (tm-30) REVERT: y 77 LEU cc_start: 0.9403 (mm) cc_final: 0.9161 (mp) REVERT: y 97 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8382 (tttp) REVERT: y 147 ASP cc_start: 0.8383 (t0) cc_final: 0.8036 (m-30) REVERT: y 148 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8832 (mtmt) REVERT: z 37 LYS cc_start: 0.8866 (tttt) cc_final: 0.8584 (ttmt) REVERT: z 52 PHE cc_start: 0.9102 (t80) cc_final: 0.8888 (t80) REVERT: z 65 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8689 (tm-30) REVERT: z 74 GLU cc_start: 0.7743 (tt0) cc_final: 0.7164 (tt0) REVERT: z 86 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8276 (ttpp) REVERT: z 97 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8262 (tttp) REVERT: z 102 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7839 (tp) REVERT: z 109 GLU cc_start: 0.8122 (mp0) cc_final: 0.7749 (mp0) REVERT: z 147 ASP cc_start: 0.8191 (t0) cc_final: 0.7777 (m-30) REVERT: 1 58 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: 1 65 GLN cc_start: 0.9349 (tm-30) cc_final: 0.8783 (tm-30) REVERT: 1 85 GLU cc_start: 0.7987 (tp30) cc_final: 0.7672 (tm-30) REVERT: 1 86 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8563 (mtpt) REVERT: 1 97 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8405 (tttp) REVERT: 1 147 ASP cc_start: 0.8388 (t0) cc_final: 0.8062 (m-30) REVERT: 1 148 LYS cc_start: 0.9245 (mtpt) cc_final: 0.8832 (mtmt) REVERT: 3 65 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8600 (tm-30) REVERT: 3 70 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.8492 (mtt-85) REVERT: 3 81 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7458 (tm-30) REVERT: 3 82 GLU cc_start: 0.8518 (mp0) cc_final: 0.7902 (mp0) REVERT: 3 86 LYS cc_start: 0.8422 (ttpt) cc_final: 0.8036 (ttpp) REVERT: 3 97 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8370 (tttp) REVERT: 3 102 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7870 (tp) REVERT: 3 147 ASP cc_start: 0.8254 (t0) cc_final: 0.7916 (m-30) REVERT: 5 58 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.6235 (m-10) REVERT: 5 65 GLN cc_start: 0.9350 (tm-30) cc_final: 0.8781 (tm-30) REVERT: 5 77 LEU cc_start: 0.9418 (mm) cc_final: 0.9203 (mp) REVERT: 5 85 GLU cc_start: 0.8212 (tp30) cc_final: 0.7846 (tm-30) REVERT: 5 86 LYS cc_start: 0.8954 (ttpt) cc_final: 0.8559 (mtpt) REVERT: 5 97 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8398 (tttp) REVERT: 5 147 ASP cc_start: 0.8403 (t0) cc_final: 0.8060 (m-30) REVERT: 5 148 LYS cc_start: 0.9249 (mtpt) cc_final: 0.8921 (mtmt) REVERT: 7 65 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8137 (tm-30) REVERT: 7 81 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7434 (tm-30) REVERT: 7 82 GLU cc_start: 0.8511 (mp0) cc_final: 0.7910 (mp0) REVERT: 7 86 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8011 (ttpp) REVERT: 7 97 LYS cc_start: 0.9170 (ttpt) cc_final: 0.8386 (tttp) REVERT: 7 109 GLU cc_start: 0.8051 (mp0) cc_final: 0.7398 (mp0) REVERT: 7 138 ARG cc_start: 0.8529 (mtp85) cc_final: 0.7983 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8267 (t0) cc_final: 0.7899 (m-30) REVERT: 9 50 GLU cc_start: 0.8961 (tt0) cc_final: 0.8412 (tm-30) REVERT: 9 58 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: 9 65 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8721 (tm-30) REVERT: 9 97 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8358 (tttp) REVERT: 9 147 ASP cc_start: 0.8395 (t0) cc_final: 0.8032 (m-30) REVERT: 9 148 LYS cc_start: 0.9243 (mtpt) cc_final: 0.8844 (mtmt) REVERT: 9 171 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6722 (pmtt) REVERT: A 354 ASP cc_start: 0.7970 (m-30) cc_final: 0.7597 (m-30) REVERT: D 354 ASP cc_start: 0.8038 (m-30) cc_final: 0.7620 (m-30) REVERT: D 359 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7535 (pp) REVERT: G 347 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8815 (mmtt) REVERT: J 354 ASP cc_start: 0.8051 (m-30) cc_final: 0.7597 (m-30) REVERT: M 354 ASP cc_start: 0.7916 (m-30) cc_final: 0.7462 (m-30) REVERT: P 354 ASP cc_start: 0.8027 (m-30) cc_final: 0.7629 (m-30) REVERT: S 354 ASP cc_start: 0.7908 (m-30) cc_final: 0.7567 (m-30) REVERT: U 359 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7339 (pp) REVERT: B 343 ASP cc_start: 0.7863 (p0) cc_final: 0.7434 (p0) REVERT: E 358 MET cc_start: 0.8275 (tpp) cc_final: 0.7970 (tpp) REVERT: E 362 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8663 (mmtt) REVERT: H 343 ASP cc_start: 0.8043 (p0) cc_final: 0.7667 (p0) REVERT: H 358 MET cc_start: 0.8321 (tpp) cc_final: 0.8068 (tpp) REVERT: K 343 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7783 (p0) REVERT: K 358 MET cc_start: 0.8144 (tpp) cc_final: 0.7881 (tpp) REVERT: N 358 MET cc_start: 0.8303 (tpp) cc_final: 0.8052 (tpp) REVERT: Q 343 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7752 (p0) REVERT: Q 353 LYS cc_start: 0.9024 (pttt) cc_final: 0.8555 (mmmt) REVERT: Q 358 MET cc_start: 0.8428 (tpp) cc_final: 0.8172 (tpp) REVERT: T 343 ASP cc_start: 0.7917 (p0) cc_final: 0.7501 (p0) REVERT: T 345 LYS cc_start: 0.4868 (tptt) cc_final: 0.4398 (tptt) REVERT: T 358 MET cc_start: 0.8321 (tpp) cc_final: 0.8055 (tpp) REVERT: V 343 ASP cc_start: 0.8283 (p0) cc_final: 0.8056 (p0) REVERT: V 358 MET cc_start: 0.8189 (tpp) cc_final: 0.7865 (tpp) outliers start: 143 outliers final: 92 residues processed: 1028 average time/residue: 0.3745 time to fit residues: 572.9861 Evaluate side-chains 1038 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 931 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 37 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 118 GLU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 160 GLU Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 160 GLU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 118 GLU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 160 GLU Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain P residue 360 ASN Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain U residue 359 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 340 ILE Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN 1 41 GLN 5 41 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 360 ASN ** S 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22224 Z= 0.212 Angle : 0.676 8.970 30080 Z= 0.360 Chirality : 0.045 0.156 3392 Planarity : 0.005 0.050 3744 Dihedral : 6.990 59.924 2968 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 5.58 % Allowed : 29.79 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2624 helix: 0.44 (0.17), residues: 976 sheet: -0.34 (0.21), residues: 672 loop : -2.81 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 364 HIS 0.002 0.001 HIS P 363 PHE 0.025 0.002 PHE 3 48 TYR 0.019 0.001 TYR 2 96 ARG 0.007 0.001 ARG 8 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 930 time to evaluate : 2.734 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: X 85 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8192 (tm-30) REVERT: X 88 THR cc_start: 0.9442 (m) cc_final: 0.9130 (p) REVERT: X 133 ASN cc_start: 0.8975 (m-40) cc_final: 0.8391 (t0) REVERT: Y 37 LYS cc_start: 0.9274 (tmtt) cc_final: 0.8769 (tptp) REVERT: Y 85 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8243 (tm-30) REVERT: Y 88 THR cc_start: 0.9559 (m) cc_final: 0.9236 (p) REVERT: Y 96 TYR cc_start: 0.8955 (t80) cc_final: 0.8667 (t80) REVERT: Y 133 ASN cc_start: 0.8869 (m-40) cc_final: 0.8511 (t0) REVERT: Y 138 ARG cc_start: 0.8593 (ptp-110) cc_final: 0.8285 (mtm110) REVERT: Z 85 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8287 (tm-30) REVERT: Z 88 THR cc_start: 0.9416 (m) cc_final: 0.9087 (p) REVERT: Z 133 ASN cc_start: 0.8985 (m-40) cc_final: 0.8539 (t0) REVERT: 0 37 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8772 (tptp) REVERT: 0 50 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8105 (pp20) REVERT: 0 85 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8339 (tm-30) REVERT: 0 88 THR cc_start: 0.9529 (m) cc_final: 0.9194 (p) REVERT: 0 133 ASN cc_start: 0.8909 (m-40) cc_final: 0.8450 (t0) REVERT: 0 138 ARG cc_start: 0.8620 (ptp-110) cc_final: 0.8285 (mtm110) REVERT: 2 65 GLN cc_start: 0.8059 (tt0) cc_final: 0.7855 (tm-30) REVERT: 2 85 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8103 (tm-30) REVERT: 2 88 THR cc_start: 0.9462 (m) cc_final: 0.9118 (p) REVERT: 2 133 ASN cc_start: 0.8861 (m-40) cc_final: 0.8482 (t0) REVERT: 4 85 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8311 (tm-30) REVERT: 4 88 THR cc_start: 0.9522 (m) cc_final: 0.9206 (p) REVERT: 4 126 ILE cc_start: 0.9401 (mt) cc_final: 0.9194 (mp) REVERT: 4 133 ASN cc_start: 0.8908 (m-40) cc_final: 0.8455 (t0) REVERT: 4 138 ARG cc_start: 0.8674 (ptp-110) cc_final: 0.8327 (mtm110) REVERT: 4 144 ASN cc_start: 0.8295 (t0) cc_final: 0.6921 (p0) REVERT: 6 37 LYS cc_start: 0.9024 (tttm) cc_final: 0.8446 (tptm) REVERT: 6 85 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8100 (tm-30) REVERT: 6 88 THR cc_start: 0.9436 (m) cc_final: 0.9127 (p) REVERT: 6 133 ASN cc_start: 0.8986 (m-40) cc_final: 0.8535 (t0) REVERT: 8 85 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8264 (tm-30) REVERT: 8 88 THR cc_start: 0.9505 (m) cc_final: 0.9150 (p) REVERT: 8 117 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7672 (pp) REVERT: 8 133 ASN cc_start: 0.8897 (m-40) cc_final: 0.8436 (t0) REVERT: 8 138 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8271 (mtm110) REVERT: x 37 LYS cc_start: 0.8893 (tttt) cc_final: 0.8611 (ttmt) REVERT: x 65 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8704 (tm-30) REVERT: x 74 GLU cc_start: 0.7586 (tt0) cc_final: 0.7133 (tt0) REVERT: x 79 ASN cc_start: 0.8430 (p0) cc_final: 0.8126 (p0) REVERT: x 81 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7189 (tm-30) REVERT: x 82 GLU cc_start: 0.8552 (mp0) cc_final: 0.7817 (mp0) REVERT: x 86 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8122 (ttpp) REVERT: x 102 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7907 (tp) REVERT: x 109 GLU cc_start: 0.8181 (mp0) cc_final: 0.7918 (mp0) REVERT: x 137 HIS cc_start: 0.7841 (p-80) cc_final: 0.7632 (p-80) REVERT: x 138 ARG cc_start: 0.8531 (mtp85) cc_final: 0.7985 (mtm-85) REVERT: x 147 ASP cc_start: 0.8166 (t0) cc_final: 0.7747 (m-30) REVERT: y 58 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6356 (m-10) REVERT: y 65 GLN cc_start: 0.9297 (tm-30) cc_final: 0.8717 (tm-30) REVERT: y 97 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8379 (tttp) REVERT: y 138 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8100 (mtm-85) REVERT: y 147 ASP cc_start: 0.8399 (t0) cc_final: 0.8090 (m-30) REVERT: y 148 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8816 (mtmt) REVERT: z 37 LYS cc_start: 0.8855 (tttt) cc_final: 0.8558 (ttmt) REVERT: z 65 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8717 (tm-30) REVERT: z 74 GLU cc_start: 0.7750 (tt0) cc_final: 0.7156 (tt0) REVERT: z 86 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8053 (ttpp) REVERT: z 97 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8295 (tttp) REVERT: z 102 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7914 (tp) REVERT: z 109 GLU cc_start: 0.8124 (mp0) cc_final: 0.7817 (mp0) REVERT: z 147 ASP cc_start: 0.8209 (t0) cc_final: 0.7807 (m-30) REVERT: z 171 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6461 (pmtt) REVERT: 1 52 PHE cc_start: 0.9263 (t80) cc_final: 0.8936 (t80) REVERT: 1 58 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.6222 (m-10) REVERT: 1 65 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8761 (tm-30) REVERT: 1 85 GLU cc_start: 0.8143 (tp30) cc_final: 0.7685 (tm-30) REVERT: 1 86 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8577 (mtpt) REVERT: 1 97 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8366 (tttp) REVERT: 1 147 ASP cc_start: 0.8414 (t0) cc_final: 0.8093 (m-30) REVERT: 1 148 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8808 (mtmt) REVERT: 3 65 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8901 (tm-30) REVERT: 3 79 ASN cc_start: 0.8446 (p0) cc_final: 0.8211 (p0) REVERT: 3 81 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7482 (tm-30) REVERT: 3 82 GLU cc_start: 0.8585 (mp0) cc_final: 0.7748 (mp0) REVERT: 3 86 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8079 (ttpp) REVERT: 3 97 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8265 (tttp) REVERT: 3 102 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7896 (tp) REVERT: 3 137 HIS cc_start: 0.7760 (p-80) cc_final: 0.7560 (p-80) REVERT: 3 147 ASP cc_start: 0.8291 (t0) cc_final: 0.7929 (m-30) REVERT: 5 58 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.6204 (m-10) REVERT: 5 65 GLN cc_start: 0.9340 (tm-30) cc_final: 0.8758 (tm-30) REVERT: 5 86 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8582 (mtpt) REVERT: 5 97 LYS cc_start: 0.9047 (ttmt) cc_final: 0.8330 (tttm) REVERT: 5 147 ASP cc_start: 0.8418 (t0) cc_final: 0.8089 (m-30) REVERT: 5 148 LYS cc_start: 0.9247 (mtpt) cc_final: 0.8812 (mtmt) REVERT: 7 65 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8673 (tm-30) REVERT: 7 79 ASN cc_start: 0.8434 (p0) cc_final: 0.8215 (p0) REVERT: 7 81 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7440 (tm-30) REVERT: 7 82 GLU cc_start: 0.8587 (mp0) cc_final: 0.7858 (mp0) REVERT: 7 86 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8011 (ttpp) REVERT: 7 97 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8183 (tttp) REVERT: 7 109 GLU cc_start: 0.8029 (mp0) cc_final: 0.7624 (mp0) REVERT: 7 138 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8027 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8276 (t0) cc_final: 0.7920 (m-30) REVERT: 9 50 GLU cc_start: 0.8971 (tt0) cc_final: 0.8432 (tm-30) REVERT: 9 52 PHE cc_start: 0.9208 (t80) cc_final: 0.8949 (t80) REVERT: 9 58 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.6222 (m-10) REVERT: 9 65 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8673 (tm-30) REVERT: 9 97 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8381 (tttm) REVERT: 9 138 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8081 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8425 (t0) cc_final: 0.8085 (m-30) REVERT: 9 148 LYS cc_start: 0.9248 (mtpt) cc_final: 0.8817 (mtmt) REVERT: 9 171 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6878 (pmtt) REVERT: A 354 ASP cc_start: 0.8014 (m-30) cc_final: 0.7616 (m-30) REVERT: G 347 LYS cc_start: 0.9059 (mmtp) cc_final: 0.8820 (mmtt) REVERT: M 354 ASP cc_start: 0.7915 (m-30) cc_final: 0.7469 (m-30) REVERT: P 354 ASP cc_start: 0.8138 (m-30) cc_final: 0.7738 (m-30) REVERT: P 358 MET cc_start: 0.8152 (ttm) cc_final: 0.7773 (ttm) REVERT: S 354 ASP cc_start: 0.7964 (m-30) cc_final: 0.7585 (m-30) REVERT: B 343 ASP cc_start: 0.7882 (p0) cc_final: 0.7463 (p0) REVERT: B 358 MET cc_start: 0.8552 (tpp) cc_final: 0.7899 (mpp) REVERT: E 358 MET cc_start: 0.8240 (tpp) cc_final: 0.7971 (tpp) REVERT: H 343 ASP cc_start: 0.8040 (p0) cc_final: 0.7712 (p0) REVERT: H 358 MET cc_start: 0.8337 (tpp) cc_final: 0.8043 (tpp) REVERT: K 343 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7795 (p0) REVERT: N 343 ASP cc_start: 0.8003 (p0) cc_final: 0.7668 (p0) REVERT: N 358 MET cc_start: 0.8282 (tpp) cc_final: 0.8000 (tpp) REVERT: Q 343 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7784 (p0) REVERT: Q 353 LYS cc_start: 0.9047 (pttt) cc_final: 0.8567 (mmmt) REVERT: Q 358 MET cc_start: 0.8491 (tpp) cc_final: 0.8203 (tpp) REVERT: T 343 ASP cc_start: 0.7945 (p0) cc_final: 0.7548 (p0) REVERT: T 358 MET cc_start: 0.8306 (tpp) cc_final: 0.8018 (tpp) REVERT: V 343 ASP cc_start: 0.8319 (p0) cc_final: 0.8091 (p0) outliers start: 134 outliers final: 100 residues processed: 1007 average time/residue: 0.3757 time to fit residues: 560.0405 Evaluate side-chains 1029 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 916 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 4 residue 160 GLU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 102 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 50 GLU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 84 LEU Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 102 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 118 GLU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 1 residue 160 GLU Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 43 ASP Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 160 GLU Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 84 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 118 GLU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain P residue 360 ASN Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain N residue 340 ILE Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 217 optimal weight: 0.0030 chunk 150 optimal weight: 0.8980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN ** z 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 41 GLN 5 41 GLN G 360 ASN J 360 ASN M 360 ASN S 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22224 Z= 0.212 Angle : 0.701 8.925 30080 Z= 0.374 Chirality : 0.045 0.155 3392 Planarity : 0.005 0.050 3744 Dihedral : 6.937 59.768 2968 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 5.12 % Allowed : 30.58 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2624 helix: 0.52 (0.17), residues: 976 sheet: -0.24 (0.21), residues: 672 loop : -2.77 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 364 HIS 0.002 0.001 HIS z 137 PHE 0.024 0.002 PHE 3 48 TYR 0.020 0.001 TYR P 349 ARG 0.008 0.001 ARG 0 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 932 time to evaluate : 2.996 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: X 85 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8307 (tm-30) REVERT: X 88 THR cc_start: 0.9440 (m) cc_final: 0.9132 (p) REVERT: X 133 ASN cc_start: 0.8970 (m-40) cc_final: 0.8395 (t0) REVERT: Y 37 LYS cc_start: 0.9246 (tmtt) cc_final: 0.8763 (tptp) REVERT: Y 85 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8228 (tm-30) REVERT: Y 88 THR cc_start: 0.9550 (m) cc_final: 0.9219 (p) REVERT: Y 133 ASN cc_start: 0.8853 (m-40) cc_final: 0.8510 (t0) REVERT: Y 138 ARG cc_start: 0.8605 (ptp-110) cc_final: 0.8299 (mtm110) REVERT: Z 37 LYS cc_start: 0.8786 (tttm) cc_final: 0.8355 (tptm) REVERT: Z 85 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8294 (tm-30) REVERT: Z 88 THR cc_start: 0.9410 (m) cc_final: 0.9083 (p) REVERT: Z 133 ASN cc_start: 0.8996 (m-40) cc_final: 0.8550 (t0) REVERT: 0 37 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8847 (tptp) REVERT: 0 50 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8204 (pp20) REVERT: 0 85 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8342 (tm-30) REVERT: 0 88 THR cc_start: 0.9524 (m) cc_final: 0.9193 (p) REVERT: 0 133 ASN cc_start: 0.8875 (m-40) cc_final: 0.8490 (t0) REVERT: 0 138 ARG cc_start: 0.8634 (ptp-110) cc_final: 0.8302 (mtm110) REVERT: 2 37 LYS cc_start: 0.8772 (tptp) cc_final: 0.8461 (tptt) REVERT: 2 85 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8075 (tm-30) REVERT: 2 88 THR cc_start: 0.9462 (m) cc_final: 0.9148 (p) REVERT: 2 133 ASN cc_start: 0.8991 (m-40) cc_final: 0.8551 (t0) REVERT: 4 37 LYS cc_start: 0.8963 (tptp) cc_final: 0.8640 (tptt) REVERT: 4 50 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8188 (pp20) REVERT: 4 85 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8305 (tm-30) REVERT: 4 88 THR cc_start: 0.9525 (m) cc_final: 0.9201 (p) REVERT: 4 126 ILE cc_start: 0.9402 (mt) cc_final: 0.9189 (mp) REVERT: 4 133 ASN cc_start: 0.8866 (m-40) cc_final: 0.8502 (t0) REVERT: 4 138 ARG cc_start: 0.8667 (ptp-110) cc_final: 0.8336 (mtm110) REVERT: 4 144 ASN cc_start: 0.8196 (t0) cc_final: 0.6851 (p0) REVERT: 6 85 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8108 (tm-30) REVERT: 6 88 THR cc_start: 0.9459 (m) cc_final: 0.9151 (p) REVERT: 6 133 ASN cc_start: 0.8998 (m-40) cc_final: 0.8547 (t0) REVERT: 8 37 LYS cc_start: 0.9038 (tptp) cc_final: 0.8230 (tptp) REVERT: 8 85 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8321 (tm-30) REVERT: 8 88 THR cc_start: 0.9496 (m) cc_final: 0.9148 (p) REVERT: 8 117 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7626 (pp) REVERT: 8 128 TYR cc_start: 0.9103 (t80) cc_final: 0.8896 (t80) REVERT: 8 133 ASN cc_start: 0.8862 (m-40) cc_final: 0.8372 (t0) REVERT: 8 138 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8299 (mtm110) REVERT: x 37 LYS cc_start: 0.8868 (tttt) cc_final: 0.8591 (ttmt) REVERT: x 65 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8678 (tm-30) REVERT: x 74 GLU cc_start: 0.7590 (tt0) cc_final: 0.7143 (tt0) REVERT: x 79 ASN cc_start: 0.8416 (p0) cc_final: 0.8183 (p0) REVERT: x 81 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7154 (tm-30) REVERT: x 82 GLU cc_start: 0.8451 (mp0) cc_final: 0.7723 (mp0) REVERT: x 97 LYS cc_start: 0.9219 (ttpt) cc_final: 0.8380 (tttp) REVERT: x 109 GLU cc_start: 0.8175 (mp0) cc_final: 0.7908 (mp0) REVERT: x 138 ARG cc_start: 0.8546 (mtp85) cc_final: 0.7995 (mtm-85) REVERT: x 147 ASP cc_start: 0.8318 (t0) cc_final: 0.7905 (m-30) REVERT: y 58 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6271 (m-10) REVERT: y 65 GLN cc_start: 0.9351 (tm-30) cc_final: 0.8796 (tm-30) REVERT: y 97 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8296 (tttp) REVERT: y 138 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8099 (mtm-85) REVERT: y 147 ASP cc_start: 0.8406 (t0) cc_final: 0.8111 (m-30) REVERT: y 148 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8807 (mtmt) REVERT: z 37 LYS cc_start: 0.8855 (tttt) cc_final: 0.8551 (ttmt) REVERT: z 65 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8740 (tm-30) REVERT: z 74 GLU cc_start: 0.7581 (tt0) cc_final: 0.7073 (tt0) REVERT: z 86 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8070 (ttpp) REVERT: z 97 LYS cc_start: 0.9130 (ttpt) cc_final: 0.8471 (tttp) REVERT: z 102 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7920 (tp) REVERT: z 109 GLU cc_start: 0.8045 (mp0) cc_final: 0.7811 (mp0) REVERT: z 147 ASP cc_start: 0.8347 (t0) cc_final: 0.7934 (m-30) REVERT: z 171 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6752 (pmtt) REVERT: 1 52 PHE cc_start: 0.9213 (t80) cc_final: 0.8906 (t80) REVERT: 1 58 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.6229 (m-10) REVERT: 1 65 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8797 (tm-30) REVERT: 1 85 GLU cc_start: 0.7946 (tp30) cc_final: 0.7690 (tm-30) REVERT: 1 97 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8378 (tttp) REVERT: 1 147 ASP cc_start: 0.8425 (t0) cc_final: 0.8117 (m-30) REVERT: 1 148 LYS cc_start: 0.9217 (mtpt) cc_final: 0.8804 (mtmt) REVERT: 3 81 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7488 (tm-30) REVERT: 3 82 GLU cc_start: 0.8548 (mp0) cc_final: 0.7904 (mp0) REVERT: 3 86 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8269 (ttpp) REVERT: 3 97 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8347 (tttp) REVERT: 3 102 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7891 (tp) REVERT: 3 147 ASP cc_start: 0.8276 (t0) cc_final: 0.7942 (m-30) REVERT: 5 52 PHE cc_start: 0.9241 (t80) cc_final: 0.8875 (t80) REVERT: 5 58 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: 5 65 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8800 (tm-30) REVERT: 5 86 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8405 (ttpp) REVERT: 5 97 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8303 (tttm) REVERT: 5 147 ASP cc_start: 0.8425 (t0) cc_final: 0.8109 (m-30) REVERT: 5 148 LYS cc_start: 0.9218 (mtpt) cc_final: 0.8803 (mtmt) REVERT: 7 65 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8698 (tm-30) REVERT: 7 79 ASN cc_start: 0.8420 (p0) cc_final: 0.8190 (p0) REVERT: 7 81 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7487 (tm-30) REVERT: 7 82 GLU cc_start: 0.8580 (mp0) cc_final: 0.7911 (mp0) REVERT: 7 86 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8071 (ttpp) REVERT: 7 97 LYS cc_start: 0.9153 (ttpt) cc_final: 0.8228 (tttp) REVERT: 7 109 GLU cc_start: 0.8025 (mp0) cc_final: 0.7609 (mp0) REVERT: 7 147 ASP cc_start: 0.8329 (t0) cc_final: 0.7875 (m-30) REVERT: 9 50 GLU cc_start: 0.8947 (tt0) cc_final: 0.8477 (tm-30) REVERT: 9 58 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: 9 65 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8712 (tm-30) REVERT: 9 97 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8386 (tttp) REVERT: 9 138 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8076 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8435 (t0) cc_final: 0.8111 (m-30) REVERT: 9 148 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8798 (mtmt) REVERT: 9 171 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6602 (pmtt) REVERT: A 354 ASP cc_start: 0.7914 (m-30) cc_final: 0.7529 (m-30) REVERT: G 347 LYS cc_start: 0.9067 (mmtp) cc_final: 0.8822 (mmtt) REVERT: J 345 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8162 (tppt) REVERT: M 354 ASP cc_start: 0.7944 (m-30) cc_final: 0.7460 (m-30) REVERT: S 354 ASP cc_start: 0.7949 (m-30) cc_final: 0.7569 (m-30) REVERT: B 343 ASP cc_start: 0.7926 (p0) cc_final: 0.7546 (p0) REVERT: B 358 MET cc_start: 0.8549 (tpp) cc_final: 0.7834 (mpp) REVERT: H 358 MET cc_start: 0.8321 (tpp) cc_final: 0.8038 (tpp) REVERT: K 343 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7799 (p0) REVERT: N 343 ASP cc_start: 0.7991 (p0) cc_final: 0.7689 (p0) REVERT: N 358 MET cc_start: 0.8246 (tpp) cc_final: 0.7978 (tpp) REVERT: Q 343 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7795 (p0) REVERT: Q 353 LYS cc_start: 0.9030 (pttt) cc_final: 0.8552 (mmmt) REVERT: Q 358 MET cc_start: 0.8575 (tpp) cc_final: 0.8257 (tpp) REVERT: T 358 MET cc_start: 0.8272 (tpp) cc_final: 0.7981 (tpp) REVERT: V 343 ASP cc_start: 0.8311 (p0) cc_final: 0.8091 (p0) outliers start: 123 outliers final: 100 residues processed: 999 average time/residue: 0.3749 time to fit residues: 554.1771 Evaluate side-chains 1032 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 920 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 35 ILE Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 131 ASP Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 141 ILE Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 50 GLU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 118 GLU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 43 ASP Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 160 GLU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 43 ASP Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 160 GLU Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 43 ASP Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 118 GLU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.0570 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 255 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 79 ASN J 360 ASN ** M 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22224 Z= 0.234 Angle : 0.721 8.984 30080 Z= 0.383 Chirality : 0.045 0.158 3392 Planarity : 0.005 0.052 3744 Dihedral : 6.896 59.970 2968 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.12 % Allowed : 31.38 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2624 helix: 0.59 (0.18), residues: 960 sheet: -0.20 (0.21), residues: 672 loop : -2.72 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 364 HIS 0.003 0.001 HIS J 363 PHE 0.025 0.002 PHE 3 48 TYR 0.034 0.002 TYR 6 96 ARG 0.007 0.001 ARG 0 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 910 time to evaluate : 2.684 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: X 41 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8412 (mm-40) REVERT: X 85 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8236 (tm-30) REVERT: X 88 THR cc_start: 0.9461 (m) cc_final: 0.9153 (p) REVERT: X 133 ASN cc_start: 0.8945 (m-40) cc_final: 0.8394 (t0) REVERT: Y 85 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8224 (tm-30) REVERT: Y 88 THR cc_start: 0.9547 (m) cc_final: 0.9230 (p) REVERT: Y 96 TYR cc_start: 0.8946 (t80) cc_final: 0.8661 (t80) REVERT: Y 126 ILE cc_start: 0.9404 (mt) cc_final: 0.9195 (mp) REVERT: Y 133 ASN cc_start: 0.8894 (m-40) cc_final: 0.8565 (t0) REVERT: Y 138 ARG cc_start: 0.8651 (ptp-110) cc_final: 0.8340 (mtm110) REVERT: Z 85 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8297 (tm-30) REVERT: Z 88 THR cc_start: 0.9431 (m) cc_final: 0.9099 (p) REVERT: Z 133 ASN cc_start: 0.8992 (m-40) cc_final: 0.8560 (t0) REVERT: 0 37 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8842 (tptp) REVERT: 0 50 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8227 (pp20) REVERT: 0 85 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8346 (tm-30) REVERT: 0 88 THR cc_start: 0.9524 (m) cc_final: 0.9146 (p) REVERT: 0 133 ASN cc_start: 0.8898 (m-40) cc_final: 0.8565 (t0) REVERT: 0 138 ARG cc_start: 0.8671 (ptp-110) cc_final: 0.8315 (mtm110) REVERT: 2 37 LYS cc_start: 0.8747 (tptp) cc_final: 0.8541 (tptp) REVERT: 2 85 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8087 (tm-30) REVERT: 2 88 THR cc_start: 0.9476 (m) cc_final: 0.9157 (p) REVERT: 2 133 ASN cc_start: 0.8993 (m-40) cc_final: 0.8562 (t0) REVERT: 4 37 LYS cc_start: 0.9000 (tptp) cc_final: 0.8479 (tptp) REVERT: 4 50 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8236 (pp20) REVERT: 4 85 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8304 (tm-30) REVERT: 4 88 THR cc_start: 0.9521 (m) cc_final: 0.9196 (p) REVERT: 4 126 ILE cc_start: 0.9408 (mt) cc_final: 0.9194 (mp) REVERT: 4 133 ASN cc_start: 0.8872 (m-40) cc_final: 0.8511 (t0) REVERT: 4 138 ARG cc_start: 0.8669 (ptp-110) cc_final: 0.8312 (mtm110) REVERT: 4 144 ASN cc_start: 0.8319 (t0) cc_final: 0.6901 (p0) REVERT: 6 85 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8103 (tm-30) REVERT: 6 88 THR cc_start: 0.9476 (m) cc_final: 0.9161 (p) REVERT: 6 133 ASN cc_start: 0.8996 (m-40) cc_final: 0.8567 (t0) REVERT: 8 37 LYS cc_start: 0.9030 (tptp) cc_final: 0.8352 (tptp) REVERT: 8 85 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8322 (tm-30) REVERT: 8 88 THR cc_start: 0.9501 (m) cc_final: 0.9147 (p) REVERT: 8 96 TYR cc_start: 0.8936 (t80) cc_final: 0.8632 (t80) REVERT: 8 117 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7667 (pp) REVERT: 8 128 TYR cc_start: 0.9091 (t80) cc_final: 0.8599 (t80) REVERT: 8 133 ASN cc_start: 0.8893 (m-40) cc_final: 0.8435 (t0) REVERT: 8 138 ARG cc_start: 0.8681 (ptp-110) cc_final: 0.8336 (mtm110) REVERT: x 37 LYS cc_start: 0.8871 (tttt) cc_final: 0.8589 (ttmt) REVERT: x 65 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8681 (tm-30) REVERT: x 74 GLU cc_start: 0.7594 (tt0) cc_final: 0.7119 (tt0) REVERT: x 79 ASN cc_start: 0.8413 (p0) cc_final: 0.8184 (p0) REVERT: x 81 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7338 (tm-30) REVERT: x 82 GLU cc_start: 0.8418 (mp0) cc_final: 0.7703 (mp0) REVERT: x 97 LYS cc_start: 0.9236 (ttpt) cc_final: 0.8369 (tttp) REVERT: x 109 GLU cc_start: 0.8170 (mp0) cc_final: 0.7890 (mp0) REVERT: x 138 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8000 (mtm-85) REVERT: x 147 ASP cc_start: 0.8237 (t0) cc_final: 0.7810 (m-30) REVERT: y 58 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.6322 (m-10) REVERT: y 65 GLN cc_start: 0.9348 (tm-30) cc_final: 0.8784 (tm-30) REVERT: y 97 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8304 (tttp) REVERT: y 138 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8097 (mtm-85) REVERT: y 147 ASP cc_start: 0.8419 (t0) cc_final: 0.8132 (m-30) REVERT: y 148 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8798 (mtmt) REVERT: z 37 LYS cc_start: 0.8847 (tttt) cc_final: 0.8522 (ttmt) REVERT: z 65 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8739 (tm-30) REVERT: z 74 GLU cc_start: 0.7580 (tt0) cc_final: 0.7034 (tt0) REVERT: z 86 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8016 (ttpp) REVERT: z 97 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8392 (tttp) REVERT: z 102 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7991 (tp) REVERT: z 109 GLU cc_start: 0.8028 (mp0) cc_final: 0.7804 (mp0) REVERT: z 147 ASP cc_start: 0.8356 (t0) cc_final: 0.7938 (m-30) REVERT: z 171 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7065 (pmtt) REVERT: 1 52 PHE cc_start: 0.9169 (t80) cc_final: 0.8887 (t80) REVERT: 1 58 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.6296 (m-10) REVERT: 1 65 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8765 (tm-30) REVERT: 1 97 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8289 (tttp) REVERT: 1 147 ASP cc_start: 0.8436 (t0) cc_final: 0.8136 (m-30) REVERT: 1 148 LYS cc_start: 0.9213 (mtpt) cc_final: 0.8797 (mtmt) REVERT: 3 65 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8685 (tm-30) REVERT: 3 79 ASN cc_start: 0.8499 (p0) cc_final: 0.8271 (p0) REVERT: 3 81 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7500 (tm-30) REVERT: 3 82 GLU cc_start: 0.8550 (mp0) cc_final: 0.7791 (mp0) REVERT: 3 86 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8232 (ttpp) REVERT: 3 97 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8386 (tttp) REVERT: 3 102 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7939 (tp) REVERT: 3 147 ASP cc_start: 0.8288 (t0) cc_final: 0.7942 (m-30) REVERT: 5 52 PHE cc_start: 0.9188 (t80) cc_final: 0.8854 (t80) REVERT: 5 58 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6317 (m-10) REVERT: 5 65 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8765 (tm-30) REVERT: 5 97 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8312 (tttp) REVERT: 5 138 ARG cc_start: 0.8336 (mtp85) cc_final: 0.8028 (mtm-85) REVERT: 5 147 ASP cc_start: 0.8440 (t0) cc_final: 0.8134 (m-30) REVERT: 5 148 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8800 (mtmt) REVERT: 7 51 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7345 (mtm-85) REVERT: 7 65 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8651 (tm-30) REVERT: 7 79 ASN cc_start: 0.8426 (p0) cc_final: 0.8170 (p0) REVERT: 7 81 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7458 (tm-30) REVERT: 7 82 GLU cc_start: 0.8577 (mp0) cc_final: 0.7911 (mp0) REVERT: 7 86 LYS cc_start: 0.8432 (ttpt) cc_final: 0.8050 (ttpp) REVERT: 7 97 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8249 (tttp) REVERT: 7 109 GLU cc_start: 0.8027 (mp0) cc_final: 0.7614 (mp0) REVERT: 7 138 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8125 (mtm-85) REVERT: 7 147 ASP cc_start: 0.8299 (t0) cc_final: 0.7880 (m-30) REVERT: 9 50 GLU cc_start: 0.8956 (tt0) cc_final: 0.8461 (tm-30) REVERT: 9 58 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6361 (m-10) REVERT: 9 65 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8750 (tm-30) REVERT: 9 97 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8315 (tttp) REVERT: 9 138 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8095 (mtm-85) REVERT: 9 147 ASP cc_start: 0.8444 (t0) cc_final: 0.8135 (m-30) REVERT: 9 148 LYS cc_start: 0.9216 (mtpt) cc_final: 0.8797 (mtmt) REVERT: 9 171 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7244 (pmtt) REVERT: A 354 ASP cc_start: 0.7930 (m-30) cc_final: 0.7547 (m-30) REVERT: G 347 LYS cc_start: 0.9093 (mmtp) cc_final: 0.8842 (mmtt) REVERT: J 345 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8186 (tppt) REVERT: M 354 ASP cc_start: 0.7949 (m-30) cc_final: 0.7478 (m-30) REVERT: P 354 ASP cc_start: 0.8051 (m-30) cc_final: 0.7735 (m-30) REVERT: S 354 ASP cc_start: 0.7964 (m-30) cc_final: 0.7573 (m-30) REVERT: B 343 ASP cc_start: 0.7944 (p0) cc_final: 0.7569 (p0) REVERT: B 358 MET cc_start: 0.8560 (tpp) cc_final: 0.7905 (mpp) REVERT: H 343 ASP cc_start: 0.8021 (p0) cc_final: 0.7759 (p0) REVERT: H 358 MET cc_start: 0.8292 (tpp) cc_final: 0.8022 (tpp) REVERT: K 343 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7829 (p0) REVERT: N 343 ASP cc_start: 0.7932 (p0) cc_final: 0.7608 (p0) REVERT: N 358 MET cc_start: 0.8259 (tpp) cc_final: 0.7994 (tpp) REVERT: Q 343 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7825 (p0) REVERT: Q 353 LYS cc_start: 0.9039 (pttt) cc_final: 0.8568 (mmmt) REVERT: Q 358 MET cc_start: 0.8603 (tpp) cc_final: 0.8089 (tpp) REVERT: T 358 MET cc_start: 0.8262 (tpp) cc_final: 0.8014 (tpp) REVERT: V 343 ASP cc_start: 0.8320 (p0) cc_final: 0.8107 (p0) outliers start: 123 outliers final: 104 residues processed: 978 average time/residue: 0.3630 time to fit residues: 527.5245 Evaluate side-chains 1020 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 904 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 90 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 131 ASP Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 117 LEU Chi-restraints excluded: chain 0 residue 37 LYS Chi-restraints excluded: chain 0 residue 117 LEU Chi-restraints excluded: chain 0 residue 131 ASP Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 131 ASP Chi-restraints excluded: chain 6 residue 90 LEU Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain x residue 42 SER Chi-restraints excluded: chain x residue 50 GLU Chi-restraints excluded: chain x residue 58 TYR Chi-restraints excluded: chain x residue 90 LEU Chi-restraints excluded: chain x residue 112 SER Chi-restraints excluded: chain x residue 114 VAL Chi-restraints excluded: chain x residue 117 LEU Chi-restraints excluded: chain x residue 141 ILE Chi-restraints excluded: chain x residue 160 GLU Chi-restraints excluded: chain x residue 165 THR Chi-restraints excluded: chain x residue 168 LEU Chi-restraints excluded: chain y residue 43 ASP Chi-restraints excluded: chain y residue 50 GLU Chi-restraints excluded: chain y residue 58 TYR Chi-restraints excluded: chain y residue 87 LEU Chi-restraints excluded: chain y residue 90 LEU Chi-restraints excluded: chain y residue 117 LEU Chi-restraints excluded: chain y residue 141 ILE Chi-restraints excluded: chain y residue 160 GLU Chi-restraints excluded: chain z residue 42 SER Chi-restraints excluded: chain z residue 50 GLU Chi-restraints excluded: chain z residue 58 TYR Chi-restraints excluded: chain z residue 79 ASN Chi-restraints excluded: chain z residue 102 LEU Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain z residue 121 SER Chi-restraints excluded: chain z residue 141 ILE Chi-restraints excluded: chain z residue 165 THR Chi-restraints excluded: chain z residue 168 LEU Chi-restraints excluded: chain z residue 171 LYS Chi-restraints excluded: chain 1 residue 43 ASP Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 1 residue 58 TYR Chi-restraints excluded: chain 1 residue 77 LEU Chi-restraints excluded: chain 1 residue 84 LEU Chi-restraints excluded: chain 1 residue 87 LEU Chi-restraints excluded: chain 1 residue 90 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 141 ILE Chi-restraints excluded: chain 3 residue 42 SER Chi-restraints excluded: chain 3 residue 50 GLU Chi-restraints excluded: chain 3 residue 58 TYR Chi-restraints excluded: chain 3 residue 90 LEU Chi-restraints excluded: chain 3 residue 102 LEU Chi-restraints excluded: chain 3 residue 112 SER Chi-restraints excluded: chain 3 residue 114 VAL Chi-restraints excluded: chain 3 residue 117 LEU Chi-restraints excluded: chain 3 residue 160 GLU Chi-restraints excluded: chain 3 residue 165 THR Chi-restraints excluded: chain 3 residue 168 LEU Chi-restraints excluded: chain 5 residue 43 ASP Chi-restraints excluded: chain 5 residue 58 TYR Chi-restraints excluded: chain 5 residue 77 LEU Chi-restraints excluded: chain 5 residue 84 LEU Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 141 ILE Chi-restraints excluded: chain 5 residue 160 GLU Chi-restraints excluded: chain 7 residue 50 GLU Chi-restraints excluded: chain 7 residue 58 TYR Chi-restraints excluded: chain 7 residue 112 SER Chi-restraints excluded: chain 7 residue 114 VAL Chi-restraints excluded: chain 7 residue 117 LEU Chi-restraints excluded: chain 7 residue 141 ILE Chi-restraints excluded: chain 7 residue 160 GLU Chi-restraints excluded: chain 7 residue 165 THR Chi-restraints excluded: chain 7 residue 168 LEU Chi-restraints excluded: chain 9 residue 43 ASP Chi-restraints excluded: chain 9 residue 47 SER Chi-restraints excluded: chain 9 residue 58 TYR Chi-restraints excluded: chain 9 residue 77 LEU Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 117 LEU Chi-restraints excluded: chain 9 residue 141 ILE Chi-restraints excluded: chain 9 residue 171 LYS Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain G residue 358 MET Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain M residue 358 MET Chi-restraints excluded: chain P residue 360 ASN Chi-restraints excluded: chain S residue 358 MET Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain H residue 353 LYS Chi-restraints excluded: chain H residue 360 ASN Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain N residue 353 LYS Chi-restraints excluded: chain N residue 360 ASN Chi-restraints excluded: chain Q residue 343 ASP Chi-restraints excluded: chain Q residue 360 ASN Chi-restraints excluded: chain T residue 340 ILE Chi-restraints excluded: chain T residue 353 LYS Chi-restraints excluded: chain T residue 360 ASN Chi-restraints excluded: chain V residue 360 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 360 ASN J 360 ASN M 360 ASN P 360 ASN S 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.074237 restraints weight = 55184.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.076567 restraints weight = 28391.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.078180 restraints weight = 17753.246| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22224 Z= 0.275 Angle : 0.745 8.670 30080 Z= 0.397 Chirality : 0.046 0.171 3392 Planarity : 0.005 0.053 3744 Dihedral : 6.791 59.671 2966 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.29 % Allowed : 31.33 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2624 helix: 0.60 (0.18), residues: 960 sheet: -0.24 (0.21), residues: 672 loop : -2.72 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 364 HIS 0.003 0.001 HIS J 363 PHE 0.026 0.002 PHE 3 48 TYR 0.032 0.002 TYR Z 96 ARG 0.007 0.001 ARG 0 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7898.70 seconds wall clock time: 141 minutes 58.19 seconds (8518.19 seconds total)