Starting phenix.real_space_refine on Thu Jun 27 06:45:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brr_44841/06_2024/9brr_44841.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 387 5.16 5 C 41973 2.51 5 N 11108 2.21 5 O 12126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "l GLU 9": "OE1" <-> "OE2" Residue "l GLU 139": "OE1" <-> "OE2" Residue "n GLU 50": "OE1" <-> "OE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "1 GLU 89": "OE1" <-> "OE2" Residue "1 GLU 158": "OE1" <-> "OE2" Residue "1 GLU 193": "OE1" <-> "OE2" Residue "1 GLU 201": "OE1" <-> "OE2" Residue "1 GLU 303": "OE1" <-> "OE2" Residue "1 GLU 335": "OE1" <-> "OE2" Residue "1 GLU 401": "OE1" <-> "OE2" Residue "1 GLU 471": "OE1" <-> "OE2" Residue "0 GLU 41": "OE1" <-> "OE2" Residue "0 GLU 53": "OE1" <-> "OE2" Residue "0 GLU 197": "OE1" <-> "OE2" Residue "0 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 463": "OE1" <-> "OE2" Residue "0 GLU 572": "OE1" <-> "OE2" Residue "0 GLU 576": "OE1" <-> "OE2" Residue "0 GLU 594": "OE1" <-> "OE2" Residue "2 GLU 49": "OE1" <-> "OE2" Residue "2 GLU 134": "OE1" <-> "OE2" Residue "2 GLU 360": "OE1" <-> "OE2" Residue "2 GLU 481": "OE1" <-> "OE2" Residue "2 GLU 485": "OE1" <-> "OE2" Residue "2 TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 290": "OE1" <-> "OE2" Residue "3 GLU 305": "OE1" <-> "OE2" Residue "3 TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 408": "OE1" <-> "OE2" Residue "3 GLU 469": "OE1" <-> "OE2" Residue "3 GLU 502": "OE1" <-> "OE2" Residue "4 GLU 148": "OE1" <-> "OE2" Residue "4 GLU 201": "OE1" <-> "OE2" Residue "4 GLU 315": "OE1" <-> "OE2" Residue "4 GLU 408": "OE1" <-> "OE2" Residue "4 GLU 442": "OE1" <-> "OE2" Residue "4 GLU 453": "OE1" <-> "OE2" Residue "4 GLU 459": "OE1" <-> "OE2" Residue "4 TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 70": "OE1" <-> "OE2" Residue "5 GLU 113": "OE1" <-> "OE2" Residue "5 GLU 283": "OE1" <-> "OE2" Residue "5 GLU 305": "OE1" <-> "OE2" Residue "5 GLU 374": "OE1" <-> "OE2" Residue "5 GLU 408": "OE1" <-> "OE2" Residue "5 GLU 453": "OE1" <-> "OE2" Residue "5 GLU 459": "OE1" <-> "OE2" Residue "5 GLU 469": "OE1" <-> "OE2" Residue "5 GLU 475": "OE1" <-> "OE2" Residue "7 GLU 193": "OE1" <-> "OE2" Residue "8 GLU 37": "OE1" <-> "OE2" Residue "8 GLU 61": "OE1" <-> "OE2" Residue "8 GLU 176": "OE1" <-> "OE2" Residue "8 GLU 197": "OE1" <-> "OE2" Residue "9 GLU 97": "OE1" <-> "OE2" Residue "9 GLU 175": "OE1" <-> "OE2" Residue "9 GLU 176": "OE1" <-> "OE2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q GLU 175": "OE1" <-> "OE2" Residue "Q GLU 197": "OE1" <-> "OE2" Residue "R GLU 38": "OE1" <-> "OE2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R GLU 105": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 74": "OE1" <-> "OE2" Residue "T GLU 105": "OE1" <-> "OE2" Residue "V GLU 93": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "6 GLU 81": "OE1" <-> "OE2" Residue "U GLU 48": "OE1" <-> "OE2" Residue "U GLU 220": "OE1" <-> "OE2" Residue "U PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 258": "OE1" <-> "OE2" Residue "U GLU 358": "OE1" <-> "OE2" Residue "U GLU 416": "OE1" <-> "OE2" Residue "d ASP 12": "OD1" <-> "OD2" Residue "d TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 296": "OE1" <-> "OE2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 31": "OE1" <-> "OE2" Residue "a GLU 102": "OE1" <-> "OE2" Residue "a GLU 124": "OE1" <-> "OE2" Residue "a GLU 210": "OE1" <-> "OE2" Residue "a PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 42": "OE1" <-> "OE2" Residue "f GLU 48": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "c PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 340": "OE1" <-> "OE2" Residue "c ARG 448": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 65594 Number of models: 1 Model: "" Number of chains: 32 Chain: "b" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1484 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "1" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "0" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "2" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "3" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3610 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Chain: "4" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "5" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "7" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "6" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2931 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 9, 'TRANS': 351} Chain breaks: 1 Chain: "U" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3501 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "d" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "a" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6117 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 31, 'TRANS': 720} Chain breaks: 2 Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "p" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Time building chain proxies: 26.27, per 1000 atoms: 0.40 Number of scatterers: 65594 At special positions: 0 Unit cell: (158.215, 182.556, 299.834, 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 387 16.00 O 12126 8.00 N 11108 7.00 C 41973 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: 21.35 Conformation dependent library (CDL) restraints added in 8.6 seconds 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15520 Finding SS restraints... Secondary structure from input PDB file: 298 helices and 43 sheets defined 60.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'b' and resid 7 through 30 removed outlier: 3.797A pdb=" N TYR b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'b' and resid 36 through 43 Processing helix chain 'b' and resid 45 through 81 removed outlier: 4.068A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 90 Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.558A pdb=" N ALA b 99 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL b 100 " --> pdb=" O PHE b 96 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA b 101 " --> pdb=" O CYS b 97 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE b 102 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE b 111 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN b 113 " --> pdb=" O ILE b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 167 removed outlier: 3.533A pdb=" N GLY b 134 " --> pdb=" O ASN b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 176 Processing helix chain 'b' and resid 177 through 199 removed outlier: 3.529A pdb=" N ILE b 181 " --> pdb=" O LEU b 177 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 46 removed outlier: 4.418A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 removed outlier: 3.575A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 80 removed outlier: 3.919A pdb=" N GLY g 63 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE g 64 " --> pdb=" O VAL g 60 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 121 Processing helix chain 'g' and resid 124 through 126 No H-bonds generated for 'chain 'g' and resid 124 through 126' Processing helix chain 'g' and resid 127 through 155 removed outlier: 4.287A pdb=" N PHE g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA g 138 " --> pdb=" O ILE g 134 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU g 139 " --> pdb=" O LEU g 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU g 141 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 45 Processing helix chain 'h' and resid 51 through 63 removed outlier: 3.513A pdb=" N ILE h 57 " --> pdb=" O MET h 53 " (cutoff:3.500A) Proline residue: h 58 - end of helix Processing helix chain 'h' and resid 63 through 80 removed outlier: 3.969A pdb=" N ILE h 67 " --> pdb=" O GLY h 63 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER h 79 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 122 Processing helix chain 'h' and resid 127 through 155 removed outlier: 4.438A pdb=" N LEU h 141 " --> pdb=" O PHE h 137 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY h 142 " --> pdb=" O ALA h 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU h 143 " --> pdb=" O GLU h 139 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS h 155 " --> pdb=" O ILE h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 45 removed outlier: 3.942A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 56 Processing helix chain 'i' and resid 56 through 79 removed outlier: 3.545A pdb=" N VAL i 60 " --> pdb=" O ILE i 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY i 63 " --> pdb=" O VAL i 59 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL i 72 " --> pdb=" O TYR i 68 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA i 73 " --> pdb=" O GLY i 69 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER i 79 " --> pdb=" O LEU i 75 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 122 removed outlier: 3.687A pdb=" N ALA i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 126 removed outlier: 6.433A pdb=" N ARG i 126 " --> pdb=" O GLN i 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 123 through 126' Processing helix chain 'i' and resid 127 through 155 removed outlier: 3.850A pdb=" N LYS i 155 " --> pdb=" O ILE i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'j' and resid 62 through 79 removed outlier: 4.357A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 124 removed outlier: 4.114A pdb=" N GLN j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 155 removed outlier: 3.876A pdb=" N VAL j 140 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU j 141 " --> pdb=" O PHE j 137 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 11 through 45 removed outlier: 4.472A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET k 44 " --> pdb=" O GLY k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 55 Processing helix chain 'k' and resid 56 through 80 removed outlier: 3.643A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE k 65 " --> pdb=" O MET k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 122 removed outlier: 3.683A pdb=" N ILE k 112 " --> pdb=" O PHE k 108 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA k 122 " --> pdb=" O VAL k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 126 No H-bonds generated for 'chain 'k' and resid 124 through 126' Processing helix chain 'k' and resid 127 through 139 Processing helix chain 'k' and resid 139 through 155 removed outlier: 4.224A pdb=" N LEU k 143 " --> pdb=" O GLU k 139 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU k 152 " --> pdb=" O VAL k 148 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 Processing helix chain 'l' and resid 51 through 56 Processing helix chain 'l' and resid 57 through 78 removed outlier: 3.753A pdb=" N MET l 61 " --> pdb=" O ILE l 57 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 122 removed outlier: 4.114A pdb=" N ALA l 122 " --> pdb=" O VAL l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 153 removed outlier: 4.265A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU l 146 " --> pdb=" O GLY l 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 45 Processing helix chain 'm' and resid 48 through 52 Processing helix chain 'm' and resid 57 through 79 removed outlier: 4.003A pdb=" N MET m 61 " --> pdb=" O ILE m 57 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 120 Processing helix chain 'm' and resid 127 through 155 removed outlier: 3.964A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 45 removed outlier: 4.339A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 removed outlier: 4.629A pdb=" N ALA n 62 " --> pdb=" O PRO n 58 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 122 removed outlier: 3.834A pdb=" N ALA n 122 " --> pdb=" O VAL n 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 155 removed outlier: 4.437A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU n 146 " --> pdb=" O GLY n 142 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS n 155 " --> pdb=" O ILE n 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 45 removed outlier: 4.042A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE o 25 " --> pdb=" O SER o 21 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.502A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 122 removed outlier: 3.931A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 126 removed outlier: 7.156A pdb=" N ARG o 126 " --> pdb=" O GLN o 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 123 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 4.635A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU o 135 " --> pdb=" O MET o 131 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 255 through 266 removed outlier: 3.705A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 4.352A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 321 through 340 removed outlier: 4.393A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET 1 340 " --> pdb=" O TYR 1 336 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 366 removed outlier: 3.821A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 387 Processing helix chain '1' and resid 419 through 427 removed outlier: 3.698A pdb=" N GLY 1 427 " --> pdb=" O SER 1 423 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 442 removed outlier: 3.547A pdb=" N ALA 1 440 " --> pdb=" O ASP 1 436 " (cutoff:3.500A) Processing helix chain '1' and resid 458 through 460 No H-bonds generated for 'chain '1' and resid 458 through 460' Processing helix chain '1' and resid 461 through 469 removed outlier: 3.501A pdb=" N HIS 1 468 " --> pdb=" O TYR 1 464 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 497 removed outlier: 4.425A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 526 through 530 removed outlier: 3.587A pdb=" N ARG 1 530 " --> pdb=" O PRO 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 562 removed outlier: 4.075A pdb=" N GLN 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 1 561 " --> pdb=" O THR 1 557 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP 1 562 " --> pdb=" O THR 1 558 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 574 through 583 Processing helix chain '1' and resid 584 through 586 No H-bonds generated for 'chain '1' and resid 584 through 586' Processing helix chain '1' and resid 593 through 616 removed outlier: 3.786A pdb=" N LEU 1 615 " --> pdb=" O ALA 1 611 " (cutoff:3.500A) Processing helix chain '0' and resid 106 through 114 Processing helix chain '0' and resid 255 through 266 Processing helix chain '0' and resid 280 through 294 Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 319 through 340 removed outlier: 4.473A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 366 removed outlier: 4.005A pdb=" N TRP 0 354 " --> pdb=" O SER 0 350 " (cutoff:3.500A) Processing helix chain '0' and resid 377 through 387 Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 443 Processing helix chain '0' and resid 461 through 469 Processing helix chain '0' and resid 471 through 495 removed outlier: 3.790A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 533 through 562 removed outlier: 3.663A pdb=" N GLN 0 560 " --> pdb=" O GLU 0 556 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER 0 561 " --> pdb=" O THR 0 557 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 574 removed outlier: 3.747A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) Processing helix chain '0' and resid 574 through 584 Processing helix chain '0' and resid 585 through 587 No H-bonds generated for 'chain '0' and resid 585 through 587' Processing helix chain '0' and resid 593 through 616 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 256 through 266 removed outlier: 3.839A pdb=" N SER 2 262 " --> pdb=" O VAL 2 258 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 294 removed outlier: 4.054A pdb=" N MET 2 284 " --> pdb=" O ARG 2 280 " (cutoff:3.500A) Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 319 through 340 removed outlier: 4.401A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 365 removed outlier: 3.882A pdb=" N ARG 2 364 " --> pdb=" O GLU 2 360 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU 2 365 " --> pdb=" O ILE 2 361 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 388 removed outlier: 3.794A pdb=" N ARG 2 388 " --> pdb=" O SER 2 384 " (cutoff:3.500A) Processing helix chain '2' and resid 419 through 429 Processing helix chain '2' and resid 437 through 442 Processing helix chain '2' and resid 457 through 469 removed outlier: 4.656A pdb=" N GLU 2 463 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR 2 464 " --> pdb=" O ALA 2 460 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 497 removed outlier: 4.543A pdb=" N GLU 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE 2 492 " --> pdb=" O ASP 2 488 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 519 Processing helix chain '2' and resid 526 through 530 removed outlier: 3.919A pdb=" N ARG 2 530 " --> pdb=" O PRO 2 527 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 561 removed outlier: 4.013A pdb=" N GLN 2 560 " --> pdb=" O GLU 2 556 " (cutoff:3.500A) Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 584 Processing helix chain '2' and resid 593 through 616 Processing helix chain '3' and resid 124 through 128 Processing helix chain '3' and resid 198 through 209 Processing helix chain '3' and resid 237 through 252 removed outlier: 3.607A pdb=" N ASN 3 251 " --> pdb=" O ASP 3 247 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY 3 252 " --> pdb=" O PHE 3 248 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 255 No H-bonds generated for 'chain '3' and resid 253 through 255' Processing helix chain '3' and resid 268 through 271 removed outlier: 3.520A pdb=" N ARG 3 271 " --> pdb=" O THR 3 268 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 268 through 271' Processing helix chain '3' and resid 272 through 289 removed outlier: 4.449A pdb=" N ARG 3 276 " --> pdb=" O ILE 3 272 " (cutoff:3.500A) Processing helix chain '3' and resid 299 through 315 removed outlier: 3.688A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG 3 314 " --> pdb=" O VAL 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 357 through 360 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 removed outlier: 3.667A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 414 through 440 removed outlier: 3.831A pdb=" N VAL 3 418 " --> pdb=" O ASP 3 414 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 445 through 462 removed outlier: 3.847A pdb=" N LYS 3 460 " --> pdb=" O GLN 3 456 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 487 removed outlier: 4.000A pdb=" N PHE 3 487 " --> pdb=" O LEU 3 483 " (cutoff:3.500A) Processing helix chain '3' and resid 496 through 504 Processing helix chain '4' and resid 124 through 128 removed outlier: 3.780A pdb=" N MET 4 127 " --> pdb=" O SER 4 124 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 124 through 128' Processing helix chain '4' and resid 198 through 209 Processing helix chain '4' and resid 218 through 224 removed outlier: 3.628A pdb=" N TYR 4 222 " --> pdb=" O ASP 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 251 Processing helix chain '4' and resid 252 through 255 removed outlier: 4.477A pdb=" N ASP 4 255 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 252 through 255' Processing helix chain '4' and resid 268 through 272 Processing helix chain '4' and resid 273 through 290 Processing helix chain '4' and resid 299 through 315 removed outlier: 3.686A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 removed outlier: 3.979A pdb=" N GLY 4 322 " --> pdb=" O GLY 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 357 through 360 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 380 through 386 removed outlier: 3.758A pdb=" N HIS 4 384 " --> pdb=" O ASP 4 380 " (cutoff:3.500A) Processing helix chain '4' and resid 401 through 404 Processing helix chain '4' and resid 415 through 439 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 removed outlier: 3.507A pdb=" N MET 5 127 " --> pdb=" O SER 5 124 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU 5 128 " --> pdb=" O GLU 5 125 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 124 through 128' Processing helix chain '5' and resid 174 through 179 Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 213 through 217 removed outlier: 3.802A pdb=" N LYS 5 217 " --> pdb=" O LYS 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 220 through 224 Processing helix chain '5' and resid 237 through 252 removed outlier: 3.659A pdb=" N GLY 5 252 " --> pdb=" O PHE 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 267 through 272 Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 314 Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 357 through 360 Processing helix chain '5' and resid 363 through 373 Processing helix chain '5' and resid 380 through 386 removed outlier: 3.562A pdb=" N HIS 5 384 " --> pdb=" O ASP 5 380 " (cutoff:3.500A) Processing helix chain '5' and resid 401 through 406 removed outlier: 3.526A pdb=" N ILE 5 406 " --> pdb=" O MET 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 440 removed outlier: 3.997A pdb=" N VAL 5 438 " --> pdb=" O ALA 5 434 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY 5 440 " --> pdb=" O LYS 5 436 " (cutoff:3.500A) Processing helix chain '5' and resid 441 through 444 Processing helix chain '5' and resid 445 through 462 Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 496 through 504 removed outlier: 4.122A pdb=" N GLU 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE 5 503 " --> pdb=" O THR 5 499 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 76 removed outlier: 3.513A pdb=" N GLN 7 16 " --> pdb=" O SER 7 12 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR 7 17 " --> pdb=" O ARG 7 13 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU 7 60 " --> pdb=" O MET 7 56 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE 7 74 " --> pdb=" O ALA 7 70 " (cutoff:3.500A) Processing helix chain '7' and resid 79 through 85 Processing helix chain '7' and resid 128 through 215 removed outlier: 4.667A pdb=" N ILE 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Proline residue: 7 178 - end of helix removed outlier: 3.645A pdb=" N LYS 7 215 " --> pdb=" O ILE 7 211 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 107 removed outlier: 4.008A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS 8 107 " --> pdb=" O SER 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 removed outlier: 4.218A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU 8 128 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 160 removed outlier: 3.999A pdb=" N ALA 8 146 " --> pdb=" O PRO 8 142 " (cutoff:3.500A) Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 217 removed outlier: 3.608A pdb=" N GLN 8 206 " --> pdb=" O LEU 8 202 " (cutoff:3.500A) Proline residue: 8 209 - end of helix Processing helix chain '9' and resid 6 through 107 removed outlier: 3.933A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 4.133A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 137 through 139 No H-bonds generated for 'chain '9' and resid 137 through 139' Processing helix chain '9' and resid 140 through 160 removed outlier: 3.664A pdb=" N ALA 9 146 " --> pdb=" O PRO 9 142 " (cutoff:3.500A) Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 207 Processing helix chain '9' and resid 208 through 216 Processing helix chain 'Q' and resid 3 through 20 removed outlier: 3.790A pdb=" N VAL Q 8 " --> pdb=" O SER Q 4 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 43 Processing helix chain 'Q' and resid 44 through 106 Processing helix chain 'Q' and resid 110 through 128 removed outlier: 3.973A pdb=" N VAL Q 114 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 139 No H-bonds generated for 'chain 'Q' and resid 137 through 139' Processing helix chain 'Q' and resid 140 through 159 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 216 Processing helix chain 'R' and resid 5 through 89 removed outlier: 3.956A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 103 removed outlier: 3.991A pdb=" N VAL R 95 " --> pdb=" O ASN R 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 removed outlier: 3.617A pdb=" N ASN T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 105 removed outlier: 4.171A pdb=" N GLN T 98 " --> pdb=" O ARG T 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 89 Processing helix chain 'V' and resid 91 through 105 removed outlier: 3.683A pdb=" N VAL V 95 " --> pdb=" O ASN V 91 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 24 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 68 through 74 Processing helix chain 'X' and resid 75 through 80 Processing helix chain 'X' and resid 103 through 109 removed outlier: 3.772A pdb=" N ALA X 109 " --> pdb=" O ILE X 105 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 22 removed outlier: 3.563A pdb=" N TRP 6 19 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 27 Processing helix chain '6' and resid 48 through 79 removed outlier: 4.485A pdb=" N GLY 6 53 " --> pdb=" O ASP 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 117 through 157 removed outlier: 3.601A pdb=" N ASN 6 157 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 171 through 175 removed outlier: 3.879A pdb=" N ASP 6 174 " --> pdb=" O LYS 6 171 " (cutoff:3.500A) Processing helix chain '6' and resid 193 through 200 Processing helix chain '6' and resid 200 through 205 Processing helix chain '6' and resid 232 through 242 removed outlier: 3.917A pdb=" N ASP 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) Processing helix chain '6' and resid 254 through 311 removed outlier: 3.664A pdb=" N MET 6 258 " --> pdb=" O ASN 6 254 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP 6 261 " --> pdb=" O GLU 6 257 " (cutoff:3.500A) Proline residue: 6 278 - end of helix removed outlier: 3.646A pdb=" N GLU 6 289 " --> pdb=" O VAL 6 285 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY 6 311 " --> pdb=" O VAL 6 307 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 341 removed outlier: 4.589A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 removed outlier: 4.030A pdb=" N ALA U 28 " --> pdb=" O ALA U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 52 removed outlier: 3.793A pdb=" N ARG U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 65 Processing helix chain 'U' and resid 66 through 69 Processing helix chain 'U' and resid 76 through 84 removed outlier: 6.554A pdb=" N THR U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 104 removed outlier: 4.550A pdb=" N MET U 100 " --> pdb=" O MET U 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN U 104 " --> pdb=" O MET U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 Processing helix chain 'U' and resid 158 through 163 removed outlier: 3.623A pdb=" N TYR U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 172 removed outlier: 4.151A pdb=" N ILE U 168 " --> pdb=" O TYR U 164 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR U 170 " --> pdb=" O ASN U 166 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU U 172 " --> pdb=" O ILE U 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 221 removed outlier: 3.652A pdb=" N ARG U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA U 221 " --> pdb=" O ALA U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 233 Processing helix chain 'U' and resid 236 through 251 Processing helix chain 'U' and resid 253 through 260 Processing helix chain 'U' and resid 261 through 263 No H-bonds generated for 'chain 'U' and resid 261 through 263' Processing helix chain 'U' and resid 264 through 276 Processing helix chain 'U' and resid 279 through 296 Processing helix chain 'U' and resid 303 through 311 removed outlier: 3.730A pdb=" N LEU U 307 " --> pdb=" O GLN U 303 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 313 through 322 removed outlier: 3.664A pdb=" N GLN U 317 " --> pdb=" O LYS U 313 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN U 320 " --> pdb=" O LYS U 316 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 350 removed outlier: 3.585A pdb=" N SER U 332 " --> pdb=" O ASP U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 362 Processing helix chain 'U' and resid 372 through 378 removed outlier: 3.918A pdb=" N TRP U 376 " --> pdb=" O SER U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 384 Processing helix chain 'U' and resid 388 through 401 Processing helix chain 'U' and resid 403 through 419 Processing helix chain 'U' and resid 421 through 432 Processing helix chain 'U' and resid 432 through 442 removed outlier: 3.809A pdb=" N LEU U 436 " --> pdb=" O GLY U 432 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS U 442 " --> pdb=" O MET U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 445 through 461 Processing helix chain 'd' and resid 8 through 26 removed outlier: 4.073A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY d 22 " --> pdb=" O GLY d 18 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU d 23 " --> pdb=" O LEU d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 37 removed outlier: 3.698A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 90 through 113 removed outlier: 4.488A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 119 Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 130 through 134 Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 160 through 168 removed outlier: 4.091A pdb=" N ASP d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE d 168 " --> pdb=" O PHE d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 176 removed outlier: 3.629A pdb=" N GLU d 175 " --> pdb=" O GLN d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 200 Processing helix chain 'd' and resid 202 through 228 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 removed outlier: 3.571A pdb=" N PHE d 241 " --> pdb=" O ARG d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.945A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 280 removed outlier: 4.556A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.679A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 339 removed outlier: 4.702A pdb=" N VAL d 319 " --> pdb=" O PHE d 315 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.819A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 49 Processing helix chain 'a' and resid 51 through 76 removed outlier: 3.830A pdb=" N VAL a 55 " --> pdb=" O PHE a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 134 removed outlier: 3.645A pdb=" N LEU a 97 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA a 117 " --> pdb=" O THR a 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS a 134 " --> pdb=" O PHE a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 199 Processing helix chain 'a' and resid 233 through 248 Processing helix chain 'a' and resid 259 through 316 removed outlier: 3.955A pdb=" N ASP a 273 " --> pdb=" O ASN a 269 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP a 274 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU a 290 " --> pdb=" O ARG a 286 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN a 291 " --> pdb=" O GLN a 287 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA a 292 " --> pdb=" O ARG a 288 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA a 293 " --> pdb=" O VAL a 289 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG a 298 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL a 299 " --> pdb=" O LYS a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 351 Processing helix chain 'a' and resid 378 through 387 Processing helix chain 'a' and resid 398 through 414 removed outlier: 4.069A pdb=" N ILE a 404 " --> pdb=" O PRO a 400 " (cutoff:3.500A) Proline residue: a 407 - end of helix Processing helix chain 'a' and resid 416 through 432 removed outlier: 3.823A pdb=" N MET a 430 " --> pdb=" O PHE a 426 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU a 432 " --> pdb=" O VAL a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 439 Processing helix chain 'a' and resid 444 through 453 Processing helix chain 'a' and resid 453 through 472 removed outlier: 3.538A pdb=" N ILE a 457 " --> pdb=" O GLY a 453 " (cutoff:3.500A) Processing helix chain 'a' and resid 527 through 534 removed outlier: 6.251A pdb=" N THR a 534 " --> pdb=" O ASN a 531 " (cutoff:3.500A) Processing helix chain 'a' and resid 535 through 562 removed outlier: 4.003A pdb=" N PHE a 539 " --> pdb=" O ASN a 535 " (cutoff:3.500A) Processing helix chain 'a' and resid 562 through 571 removed outlier: 4.029A pdb=" N ASN a 566 " --> pdb=" O LEU a 562 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 3.809A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 605 removed outlier: 4.622A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU a 594 " --> pdb=" O LEU a 590 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR a 605 " --> pdb=" O LYS a 601 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 610 Processing helix chain 'a' and resid 617 through 626 removed outlier: 3.721A pdb=" N PHE a 624 " --> pdb=" O PHE a 620 " (cutoff:3.500A) Processing helix chain 'a' and resid 639 through 653 removed outlier: 3.737A pdb=" N PHE a 646 " --> pdb=" O GLY a 642 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU a 653 " --> pdb=" O VAL a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 674 removed outlier: 3.843A pdb=" N LYS a 674 " --> pdb=" O TYR a 670 " (cutoff:3.500A) Processing helix chain 'a' and resid 716 through 739 removed outlier: 4.196A pdb=" N ILE a 734 " --> pdb=" O CYS a 730 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER a 735 " --> pdb=" O LEU a 731 " (cutoff:3.500A) Processing helix chain 'a' and resid 741 through 762 Processing helix chain 'a' and resid 769 through 791 removed outlier: 5.046A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY a 776 " --> pdb=" O ALA a 772 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU a 777 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE a 778 " --> pdb=" O GLY a 774 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 812 Processing helix chain 'a' and resid 812 through 817 removed outlier: 4.401A pdb=" N PHE a 816 " --> pdb=" O PHE a 812 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 removed outlier: 3.894A pdb=" N ILE e 20 " --> pdb=" O PHE e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 70 through 80 Processing helix chain 'f' and resid 8 through 36 removed outlier: 3.616A pdb=" N TRP f 21 " --> pdb=" O VAL f 17 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 44 Processing helix chain 'f' and resid 58 through 90 removed outlier: 3.665A pdb=" N TYR f 62 " --> pdb=" O ILE f 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 443 removed outlier: 4.385A pdb=" N GLY c 422 " --> pdb=" O GLY c 418 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET c 439 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 removed outlier: 3.600A pdb=" N ASN p 330 " --> pdb=" O TYR p 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 18 through 25 removed outlier: 6.690A pdb=" N THR 1 30 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL 1 24 " --> pdb=" O VAL 1 28 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL 1 28 " --> pdb=" O VAL 1 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.693A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '0' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 28 through 32 current: chain '0' and resid 50 through 58 removed outlier: 6.586A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '3' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 60 current: chain '3' and resid 81 through 90 removed outlier: 6.957A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS 3 93 " --> pdb=" O VAL 3 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 93 through 98 current: chain '4' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 57 through 60 current: chain '4' and resid 81 through 90 removed outlier: 6.991A pdb=" N VAL 4 95 " --> pdb=" O LEU 4 87 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL 4 89 " --> pdb=" O LYS 4 93 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 6.783A pdb=" N VAL 5 95 " --> pdb=" O LEU 5 87 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL 5 89 " --> pdb=" O LYS 5 93 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS 5 93 " --> pdb=" O VAL 5 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '5' and resid 93 through 98 current: chain '9' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 164 through 167 current: chain '9' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 190 through 195 current: chain 'Q' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 164 through 167 current: chain 'Q' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain '1' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain '1' and resid 98 through 99 removed outlier: 6.540A pdb=" N ILE 1 272 " --> pdb=" O ALA 1 310 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL 1 312 " --> pdb=" O ILE 1 272 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR 1 274 " --> pdb=" O VAL 1 312 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL 1 271 " --> pdb=" O SER 1 345 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET 1 347 " --> pdb=" O VAL 1 271 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE 1 273 " --> pdb=" O MET 1 347 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR 1 246 " --> pdb=" O GLY 1 408 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL 1 410 " --> pdb=" O THR 1 246 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE 1 248 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 164 through 167 removed outlier: 3.745A pdb=" N GLY 1 154 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY 1 183 " --> pdb=" O PHE 1 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 146 through 148 removed outlier: 7.059A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 219 through 220 removed outlier: 3.847A pdb=" N GLU 1 219 " --> pdb=" O LYS 1 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 295 through 296 removed outlier: 3.830A pdb=" N GLU 1 303 " --> pdb=" O MET 1 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AA9, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 312 current: chain '0' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 408 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '0' and resid 163 through 167 removed outlier: 3.936A pdb=" N ILE 0 166 " --> pdb=" O GLY 0 154 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN 0 157 " --> pdb=" O GLU 0 134 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU 0 134 " --> pdb=" O ASN 0 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '0' and resid 146 through 147 removed outlier: 6.790A pdb=" N GLU 0 193 " --> pdb=" O THR 0 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 295 through 297 Processing sheet with id=AB4, first strand: chain '2' and resid 61 through 66 removed outlier: 4.252A pdb=" N ARG 2 56 " --> pdb=" O THR 2 63 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN 2 65 " --> pdb=" O ILE 2 54 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE 2 54 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG 2 44 " --> pdb=" O LEU 2 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 87 through 90 removed outlier: 3.533A pdb=" N VAL 2 88 " --> pdb=" O TRP 2 209 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP 2 209 " --> pdb=" O VAL 2 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 98 through 99 current: chain '2' and resid 310 through 314 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 310 through 314 current: chain '2' and resid 401 through 410 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '2' and resid 133 through 135 removed outlier: 3.717A pdb=" N GLY 2 183 " --> pdb=" O PHE 2 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 146 through 148 removed outlier: 3.557A pdb=" N SER 2 175 " --> pdb=" O GLU 2 195 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 152 through 156 removed outlier: 6.650A pdb=" N ILE 2 166 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE 2 155 " --> pdb=" O HIS 2 164 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS 2 164 " --> pdb=" O ILE 2 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 120 through 123 removed outlier: 3.570A pdb=" N THR 3 121 " --> pdb=" O LEU 3 151 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU 3 151 " --> pdb=" O THR 3 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 131 through 132 removed outlier: 6.162A pdb=" N ILE 3 229 " --> pdb=" O CYS 3 258 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE 3 260 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE 3 231 " --> pdb=" O PHE 3 260 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA 3 228 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE 3 296 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL 3 230 " --> pdb=" O ILE 3 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 3 297 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG 3 340 " --> pdb=" O ILE 3 164 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE 3 164 " --> pdb=" O ARG 3 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 169 through 170 removed outlier: 4.475A pdb=" N ILE 3 183 " --> pdb=" O ILE 3 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 192 through 193 Processing sheet with id=AC5, first strand: chain '3' and resid 375 through 376 Processing sheet with id=AC6, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AC7, first strand: chain '4' and resid 163 through 164 removed outlier: 4.243A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AC9, first strand: chain '4' and resid 191 through 193 removed outlier: 6.035A pdb=" N ILE 4 191 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '4' and resid 257 through 260 removed outlier: 6.894A pdb=" N ILE 4 229 " --> pdb=" O CYS 4 258 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE 4 260 " --> pdb=" O ILE 4 229 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE 4 231 " --> pdb=" O PHE 4 260 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL 4 293 " --> pdb=" O SER 4 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '4' and resid 375 through 376 Processing sheet with id=AD3, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AD4, first strand: chain '5' and resid 131 through 132 removed outlier: 6.353A pdb=" N PHE 5 132 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU 5 263 " --> pdb=" O PHE 5 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY 5 235 " --> pdb=" O ASN 5 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '5' and resid 191 through 193 removed outlier: 6.133A pdb=" N ILE 5 191 " --> pdb=" O LEU 5 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '7' and resid 92 through 101 Processing sheet with id=AD7, first strand: chain '8' and resid 164 through 167 Processing sheet with id=AD8, first strand: chain 'X' and resid 36 through 38 removed outlier: 3.528A pdb=" N LEU X 37 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY X 12 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN X 67 " --> pdb=" O ILE X 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 34 through 37 removed outlier: 3.696A pdb=" N VAL 6 34 " --> pdb=" O GLN 6 322 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL 6 370 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '6' and resid 92 through 93 Processing sheet with id=AE2, first strand: chain '6' and resid 215 through 218 removed outlier: 6.547A pdb=" N VAL 6 215 " --> pdb=" O ASN 6 226 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN 6 226 " --> pdb=" O VAL 6 215 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER 6 217 " --> pdb=" O LEU 6 224 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS 6 225 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 6 186 " --> pdb=" O ARG 6 249 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 325 through 333 removed outlier: 4.250A pdb=" N LEU a 12 " --> pdb=" O MET a 362 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET a 362 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 205 through 209 Processing sheet with id=AE5, first strand: chain 'a' and resid 507 through 509 Processing sheet with id=AE6, first strand: chain 'c' and resid 262 through 264 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 262 through 264 current: chain 'c' and resid 276 through 278 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 276 through 278 current: chain 'c' and resid 387 through 396 No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'c' and resid 295 through 297 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 300 through 302 current: chain 'c' and resid 313 through 326 removed outlier: 4.011A pdb=" N ALA c 322 " --> pdb=" O ALA c 335 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 331 through 335 current: chain 'c' and resid 348 through 350 3877 hydrogen bonds defined for protein. 11370 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: 24.43 Time building geometry restraints manager: 23.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10893 1.30 - 1.43: 16533 1.43 - 1.56: 38701 1.56 - 1.69: 8 1.69 - 1.82: 685 Bond restraints: 66820 Sorted by residual: bond pdb=" C ASN d 10 " pdb=" O ASN d 10 " ideal model delta sigma weight residual 1.235 1.165 0.070 1.26e-02 6.30e+03 3.11e+01 bond pdb=" C TYR k 87 " pdb=" O TYR k 87 " ideal model delta sigma weight residual 1.236 1.296 -0.059 1.15e-02 7.56e+03 2.68e+01 bond pdb=" N MET c 446 " pdb=" CA MET c 446 " ideal model delta sigma weight residual 1.458 1.490 -0.032 6.30e-03 2.52e+04 2.52e+01 bond pdb=" C PHE b 12 " pdb=" O PHE b 12 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.15e-02 7.56e+03 2.09e+01 bond pdb=" C VAL i 60 " pdb=" O VAL i 60 " ideal model delta sigma weight residual 1.237 1.290 -0.054 1.19e-02 7.06e+03 2.02e+01 ... (remaining 66815 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.56: 817 103.56 - 111.38: 27519 111.38 - 119.19: 27664 119.19 - 127.00: 33695 127.00 - 134.82: 610 Bond angle restraints: 90305 Sorted by residual: angle pdb=" N VAL b 13 " pdb=" CA VAL b 13 " pdb=" C VAL b 13 " ideal model delta sigma weight residual 110.30 102.39 7.91 9.70e-01 1.06e+00 6.65e+01 angle pdb=" N VAL b 13 " pdb=" CA VAL b 13 " pdb=" CB VAL b 13 " ideal model delta sigma weight residual 110.62 119.16 -8.54 1.09e+00 8.42e-01 6.13e+01 angle pdb=" N GLN U 38 " pdb=" CA GLN U 38 " pdb=" C GLN U 38 " ideal model delta sigma weight residual 109.54 100.15 9.39 1.37e+00 5.33e-01 4.69e+01 angle pdb=" N TYR k 87 " pdb=" CA TYR k 87 " pdb=" C TYR k 87 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.20e+00 6.94e-01 4.55e+01 angle pdb=" N TYR m 87 " pdb=" CA TYR m 87 " pdb=" C TYR m 87 " ideal model delta sigma weight residual 111.28 104.15 7.13 1.09e+00 8.42e-01 4.28e+01 ... (remaining 90300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 37307 18.02 - 36.04: 2488 36.04 - 54.06: 458 54.06 - 72.08: 84 72.08 - 90.10: 42 Dihedral angle restraints: 40379 sinusoidal: 16192 harmonic: 24187 Sorted by residual: dihedral pdb=" CA LEU 6 22 " pdb=" C LEU 6 22 " pdb=" N HIS 6 23 " pdb=" CA HIS 6 23 " ideal model delta harmonic sigma weight residual 180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA HIS c 364 " pdb=" C HIS c 364 " pdb=" N CYS c 365 " pdb=" CA CYS c 365 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA THR a 322 " pdb=" C THR a 322 " pdb=" N GLN a 323 " pdb=" CA GLN a 323 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 40376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 8468 0.059 - 0.118: 1490 0.118 - 0.177: 246 0.177 - 0.236: 26 0.236 - 0.295: 6 Chirality restraints: 10236 Sorted by residual: chirality pdb=" CA VAL e 42 " pdb=" N VAL e 42 " pdb=" C VAL e 42 " pdb=" CB VAL e 42 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU 2 90 " pdb=" CB LEU 2 90 " pdb=" CD1 LEU 2 90 " pdb=" CD2 LEU 2 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB THR n 154 " pdb=" CA THR n 154 " pdb=" OG1 THR n 154 " pdb=" CG2 THR n 154 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 10233 not shown) Planarity restraints: 11580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU k 86 " -0.027 2.00e-02 2.50e+03 5.28e-02 2.78e+01 pdb=" C LEU k 86 " 0.091 2.00e-02 2.50e+03 pdb=" O LEU k 86 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR k 87 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL i 59 " -0.025 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" C VAL i 59 " 0.083 2.00e-02 2.50e+03 pdb=" O VAL i 59 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL i 60 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR o 144 " 0.042 2.00e-02 2.50e+03 3.13e-02 1.96e+01 pdb=" CG TYR o 144 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR o 144 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR o 144 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR o 144 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR o 144 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR o 144 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR o 144 " 0.005 2.00e-02 2.50e+03 ... (remaining 11577 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 16325 2.80 - 3.33: 68443 3.33 - 3.85: 106647 3.85 - 4.38: 122318 4.38 - 4.90: 205039 Nonbonded interactions: 518772 Sorted by model distance: nonbonded pdb=" O GLY 0 278 " pdb=" NH1 ARG 0 353 " model vdw 2.279 2.520 nonbonded pdb=" O CYS b 97 " pdb=" N ALA b 99 " model vdw 2.288 2.520 nonbonded pdb=" O PRO d 92 " pdb=" OG SER d 95 " model vdw 2.315 2.440 nonbonded pdb=" O TYR U 36 " pdb=" C LEU U 37 " model vdw 2.342 3.270 nonbonded pdb=" O ASP c 450 " pdb=" O ASP c 451 " model vdw 2.367 3.040 ... (remaining 518767 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' and resid 17 through 616) selection = chain '1' selection = chain '2' } ncs_group { reference = chain '3' selection = (chain '4' and (resid 39 through 216 or resid 224 through 506)) selection = (chain '5' and (resid 39 through 216 or resid 224 through 506)) } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.780 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: 0.090 Extract box with map and model: 19.460 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 133.980 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 : 0.005 0.077 66820 Z= 0.316 Angle : 0.835 11.812 90305 Z= 0.489 Chirality : 0.047 0.295 10236 Planarity : 0.007 0.121 11580 Dihedral : 12.844 90.100 24859 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.95 % Favored : 94.69 % Rotamer: Outliers : 0.42 % Allowed : 0.67 % Favored : 98.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.09), residues: 8319 helix: 1.07 (0.08), residues: 4700 sheet: -0.77 (0.20), residues: 671 loop : -1.49 (0.12), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP e 17 HIS 0.027 0.002 HIS X 96 PHE 0.050 0.002 PHE n 90 TYR 0.075 0.002 TYR o 144 ARG 0.032 0.001 ARG 7 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2257 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 2227 time to evaluate : 5.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 43 GLU cc_start: 0.6784 (tp30) cc_final: 0.6256 (tp30) REVERT: b 172 LEU cc_start: 0.4108 (mt) cc_final: 0.3738 (mt) REVERT: g 14 PHE cc_start: 0.6429 (m-80) cc_final: 0.5807 (m-10) REVERT: h 13 PHE cc_start: 0.8086 (m-10) cc_final: 0.7636 (m-10) REVERT: h 28 MET cc_start: 0.7052 (mmm) cc_final: 0.6637 (mmm) REVERT: h 57 ILE cc_start: 0.7302 (mm) cc_final: 0.6742 (mm) REVERT: h 61 MET cc_start: 0.8198 (mtp) cc_final: 0.7803 (mmm) REVERT: h 131 MET cc_start: 0.7302 (ttp) cc_final: 0.6931 (ttp) REVERT: i 23 MET cc_start: 0.6345 (ttm) cc_final: 0.5779 (ttm) REVERT: i 41 ILE cc_start: 0.7469 (tp) cc_final: 0.7126 (tp) REVERT: i 61 MET cc_start: 0.6690 (mmm) cc_final: 0.6309 (mmt) REVERT: i 82 ASP cc_start: 0.6721 (m-30) cc_final: 0.6169 (t70) REVERT: i 84 ILE cc_start: 0.5175 (tt) cc_final: 0.4828 (pt) REVERT: i 131 MET cc_start: 0.6511 (ttp) cc_final: 0.5982 (ppp) REVERT: i 155 LYS cc_start: 0.5849 (mmtt) cc_final: 0.5287 (mmmt) REVERT: j 12 SER cc_start: 0.7542 (p) cc_final: 0.6777 (m) REVERT: j 28 MET cc_start: 0.8907 (mtp) cc_final: 0.8529 (mtp) REVERT: j 84 ILE cc_start: 0.6890 (mt) cc_final: 0.6238 (mt) REVERT: k 118 VAL cc_start: 0.8263 (t) cc_final: 0.8005 (t) REVERT: k 135 LEU cc_start: 0.4287 (tp) cc_final: 0.4072 (tt) REVERT: l 14 PHE cc_start: 0.7356 (m-80) cc_final: 0.6869 (m-80) REVERT: l 51 LEU cc_start: 0.5879 (mp) cc_final: 0.5420 (mp) REVERT: l 53 MET cc_start: 0.7804 (mmm) cc_final: 0.6277 (tmm) REVERT: l 61 MET cc_start: 0.2359 (mtp) cc_final: 0.1810 (mtp) REVERT: l 76 ILE cc_start: 0.7359 (mt) cc_final: 0.6996 (mt) REVERT: l 102 SER cc_start: 0.8015 (m) cc_final: 0.7800 (p) REVERT: l 128 PHE cc_start: 0.4954 (t80) cc_final: 0.4349 (t80) REVERT: m 16 VAL cc_start: 0.5445 (OUTLIER) cc_final: 0.5244 (t) REVERT: m 61 MET cc_start: 0.8068 (mmm) cc_final: 0.7802 (mmm) REVERT: n 45 SER cc_start: 0.6783 (t) cc_final: 0.6427 (t) REVERT: n 82 ASP cc_start: 0.7231 (m-30) cc_final: 0.4271 (m-30) REVERT: n 127 LEU cc_start: 0.6857 (mm) cc_final: 0.6022 (pp) REVERT: n 134 ILE cc_start: 0.6747 (tp) cc_final: 0.6350 (tp) REVERT: o 48 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6332 (mpt180) REVERT: o 127 LEU cc_start: 0.6883 (mm) cc_final: 0.6492 (tp) REVERT: o 144 TYR cc_start: 0.7790 (m-80) cc_final: 0.7274 (m-80) REVERT: 1 86 LEU cc_start: 0.8524 (tp) cc_final: 0.8033 (tp) REVERT: 1 151 ASP cc_start: 0.7131 (m-30) cc_final: 0.6100 (m-30) REVERT: 1 242 GLN cc_start: 0.7752 (tt0) cc_final: 0.7314 (tp40) REVERT: 1 279 GLU cc_start: 0.7531 (pm20) cc_final: 0.5663 (mm-30) REVERT: 1 297 GLU cc_start: 0.4479 (pm20) cc_final: 0.3993 (pm20) REVERT: 1 299 ASP cc_start: 0.5397 (p0) cc_final: 0.4644 (m-30) REVERT: 1 324 GLU cc_start: 0.8530 (tt0) cc_final: 0.7848 (tt0) REVERT: 1 328 TYR cc_start: 0.7669 (m-10) cc_final: 0.7256 (m-80) REVERT: 1 345 SER cc_start: 0.8936 (t) cc_final: 0.8653 (p) REVERT: 1 346 MET cc_start: 0.7669 (ttt) cc_final: 0.7187 (ttt) REVERT: 1 404 VAL cc_start: 0.9311 (t) cc_final: 0.9067 (p) REVERT: 1 494 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7023 (tp40) REVERT: 1 573 HIS cc_start: 0.6928 (m90) cc_final: 0.6559 (t-90) REVERT: 1 588 ASP cc_start: 0.4762 (t70) cc_final: 0.4537 (t70) REVERT: 1 604 LEU cc_start: 0.8243 (tp) cc_final: 0.8042 (tp) REVERT: 0 49 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7336 (mp0) REVERT: 0 53 GLU cc_start: 0.8063 (tp30) cc_final: 0.7777 (tp30) REVERT: 0 308 ARG cc_start: 0.8103 (ptt180) cc_final: 0.7716 (ptt90) REVERT: 0 411 SER cc_start: 0.8708 (t) cc_final: 0.8335 (t) REVERT: 0 456 LYS cc_start: 0.8503 (mmpt) cc_final: 0.7219 (mtmt) REVERT: 2 20 TYR cc_start: 0.5848 (t80) cc_final: 0.5645 (t80) REVERT: 2 34 MET cc_start: 0.7188 (tmm) cc_final: 0.6917 (tmm) REVERT: 2 39 MET cc_start: 0.7194 (pmm) cc_final: 0.6718 (ptp) REVERT: 2 55 ILE cc_start: 0.8115 (mm) cc_final: 0.7068 (mm) REVERT: 2 113 THR cc_start: 0.8692 (p) cc_final: 0.8232 (t) REVERT: 2 155 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (tt) REVERT: 2 167 MET cc_start: 0.8623 (pmm) cc_final: 0.7773 (pmm) REVERT: 2 227 LEU cc_start: 0.8256 (tt) cc_final: 0.8051 (tt) REVERT: 2 335 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6530 (mt-10) REVERT: 2 347 MET cc_start: 0.8598 (ttm) cc_final: 0.8252 (mtt) REVERT: 2 388 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7259 (mmm-85) REVERT: 2 472 PHE cc_start: 0.4850 (t80) cc_final: 0.4473 (t80) REVERT: 2 476 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6450 (ttm170) REVERT: 2 544 MET cc_start: 0.6615 (mtp) cc_final: 0.6408 (mtp) REVERT: 3 70 GLU cc_start: 0.7700 (pt0) cc_final: 0.7205 (pt0) REVERT: 3 87 LEU cc_start: 0.8968 (mt) cc_final: 0.8301 (mt) REVERT: 3 97 GLN cc_start: 0.9241 (pt0) cc_final: 0.8951 (pt0) REVERT: 3 105 ILE cc_start: 0.8365 (mt) cc_final: 0.8047 (mt) REVERT: 3 183 ILE cc_start: 0.9062 (mt) cc_final: 0.8602 (mt) REVERT: 3 202 ILE cc_start: 0.9021 (mt) cc_final: 0.8767 (mt) REVERT: 3 205 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7482 (tm-30) REVERT: 3 337 ARG cc_start: 0.7489 (mtp180) cc_final: 0.7162 (mtp85) REVERT: 3 374 GLU cc_start: 0.8214 (pm20) cc_final: 0.7471 (pp20) REVERT: 3 392 ILE cc_start: 0.8342 (mt) cc_final: 0.8005 (mt) REVERT: 3 402 MET cc_start: 0.8149 (mtp) cc_final: 0.7885 (ttt) REVERT: 3 423 TYR cc_start: 0.8401 (m-80) cc_final: 0.7549 (m-80) REVERT: 3 469 GLU cc_start: 0.4742 (tm-30) cc_final: 0.4417 (tm-30) REVERT: 3 491 MET cc_start: 0.6059 (mtt) cc_final: 0.5515 (ppp) REVERT: 4 97 GLN cc_start: 0.7449 (pt0) cc_final: 0.7045 (pt0) REVERT: 4 148 GLU cc_start: 0.7964 (tt0) cc_final: 0.7619 (tm-30) REVERT: 4 152 ASP cc_start: 0.7878 (t0) cc_final: 0.7617 (p0) REVERT: 4 153 ILE cc_start: 0.8701 (tt) cc_final: 0.8263 (tt) REVERT: 4 165 TYR cc_start: 0.7746 (t80) cc_final: 0.7521 (t80) REVERT: 4 168 GLU cc_start: 0.7968 (mp0) cc_final: 0.7720 (mp0) REVERT: 4 238 MET cc_start: 0.7957 (mpp) cc_final: 0.7747 (mpp) REVERT: 4 290 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6678 (pt0) REVERT: 4 336 GLU cc_start: 0.7898 (tt0) cc_final: 0.7619 (tt0) REVERT: 4 372 ILE cc_start: 0.8621 (mt) cc_final: 0.8284 (mt) REVERT: 5 78 ASP cc_start: 0.7944 (m-30) cc_final: 0.7729 (m-30) REVERT: 5 202 ILE cc_start: 0.9119 (mt) cc_final: 0.8871 (mm) REVERT: 5 240 THR cc_start: 0.8431 (m) cc_final: 0.8122 (m) REVERT: 5 245 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7956 (ttpt) REVERT: 5 382 GLN cc_start: 0.7932 (mp10) cc_final: 0.7518 (mp10) REVERT: 5 423 TYR cc_start: 0.8161 (t80) cc_final: 0.7829 (t80) REVERT: 5 435 MET cc_start: 0.7026 (mtm) cc_final: 0.6616 (mtm) REVERT: 5 458 PHE cc_start: 0.7427 (t80) cc_final: 0.6714 (t80) REVERT: 5 485 ARG cc_start: 0.7352 (mtp180) cc_final: 0.6991 (mmm160) REVERT: 5 490 GLU cc_start: 0.5800 (tm-30) cc_final: 0.5019 (mt-10) REVERT: 7 23 LEU cc_start: 0.7851 (tp) cc_final: 0.7436 (tp) REVERT: 7 54 THR cc_start: 0.7166 (m) cc_final: 0.6410 (m) REVERT: 8 44 ARG cc_start: 0.6598 (mtp180) cc_final: 0.6367 (ptm160) REVERT: 8 59 LYS cc_start: 0.7692 (mmmm) cc_final: 0.6933 (pptt) REVERT: 8 72 MET cc_start: 0.7994 (mtm) cc_final: 0.7786 (mmt) REVERT: 8 208 MET cc_start: 0.7617 (tmm) cc_final: 0.6908 (tmm) REVERT: 9 54 MET cc_start: 0.7359 (mmt) cc_final: 0.6834 (mmt) REVERT: 9 154 MET cc_start: 0.8090 (mmp) cc_final: 0.7527 (mmt) REVERT: 9 191 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8866 (ttmm) REVERT: 9 197 GLU cc_start: 0.8334 (mp0) cc_final: 0.7754 (mp0) REVERT: Q 67 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7887 (tm-30) REVERT: Q 201 ASP cc_start: 0.8764 (t0) cc_final: 0.8513 (t70) REVERT: R 32 ARG cc_start: 0.6319 (ttp80) cc_final: 0.5997 (ttp80) REVERT: R 58 LYS cc_start: 0.6440 (mttt) cc_final: 0.6055 (mmmt) REVERT: R 79 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8080 (ptp-110) REVERT: R 96 LEU cc_start: 0.9158 (tp) cc_final: 0.8826 (tp) REVERT: T 12 LEU cc_start: 0.6284 (mt) cc_final: 0.6082 (mt) REVERT: T 16 LYS cc_start: 0.8088 (mttt) cc_final: 0.6992 (tttp) REVERT: T 34 LYS cc_start: 0.8148 (tppt) cc_final: 0.7544 (mttt) REVERT: T 42 MET cc_start: 0.7627 (mtm) cc_final: 0.7421 (ppp) REVERT: V 47 TYR cc_start: 0.5890 (m-10) cc_final: 0.5617 (m-10) REVERT: V 87 SER cc_start: 0.8579 (t) cc_final: 0.8223 (p) REVERT: X 27 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7066 (tm-30) REVERT: X 51 THR cc_start: 0.8109 (m) cc_final: 0.7300 (t) REVERT: 6 66 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7233 (mt-10) REVERT: 6 82 ASP cc_start: 0.5324 (t70) cc_final: 0.4866 (m-30) REVERT: 6 109 MET cc_start: 0.7535 (tmm) cc_final: 0.6281 (mtm) REVERT: 6 298 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6586 (mtmt) REVERT: 6 335 LEU cc_start: 0.5569 (pp) cc_final: 0.5185 (pp) REVERT: U 65 MET cc_start: 0.7139 (ppp) cc_final: 0.6393 (ppp) REVERT: U 90 VAL cc_start: 0.3738 (OUTLIER) cc_final: 0.3523 (p) REVERT: U 96 MET cc_start: 0.1426 (ptm) cc_final: 0.0390 (mmt) REVERT: U 127 LEU cc_start: 0.6159 (mt) cc_final: 0.5841 (pt) REVERT: U 147 LYS cc_start: 0.6405 (mmmm) cc_final: 0.5879 (tptt) REVERT: U 156 MET cc_start: 0.6748 (ptm) cc_final: 0.6361 (ptt) REVERT: U 165 PHE cc_start: 0.7393 (m-80) cc_final: 0.7107 (m-80) REVERT: U 234 LYS cc_start: 0.6203 (tttt) cc_final: 0.5720 (mptt) REVERT: U 237 PHE cc_start: 0.6560 (p90) cc_final: 0.5878 (t80) REVERT: U 252 PHE cc_start: 0.4842 (t80) cc_final: 0.4412 (t80) REVERT: U 266 ILE cc_start: 0.5682 (mt) cc_final: 0.5395 (mt) REVERT: U 284 ILE cc_start: 0.7184 (tp) cc_final: 0.6956 (tp) REVERT: U 321 LEU cc_start: 0.8167 (mm) cc_final: 0.7954 (mt) REVERT: U 383 LEU cc_start: 0.7330 (mt) cc_final: 0.6146 (mt) REVERT: U 434 LYS cc_start: 0.5945 (pttm) cc_final: 0.5330 (tttp) REVERT: d 13 ASN cc_start: 0.5256 (OUTLIER) cc_final: 0.4411 (t0) REVERT: d 38 GLN cc_start: 0.6213 (mm-40) cc_final: 0.5123 (pp30) REVERT: d 71 ASP cc_start: 0.6843 (t0) cc_final: 0.6503 (t0) REVERT: d 75 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8032 (mmmt) REVERT: d 78 MET cc_start: 0.8660 (tmm) cc_final: 0.8449 (tmm) REVERT: d 84 HIS cc_start: 0.7939 (t70) cc_final: 0.7597 (t-170) REVERT: d 128 LYS cc_start: 0.8546 (mmpt) cc_final: 0.8267 (mmpt) REVERT: d 135 PHE cc_start: 0.2870 (m-10) cc_final: 0.1739 (m-10) REVERT: d 165 GLN cc_start: 0.7222 (tt0) cc_final: 0.6225 (tp-100) REVERT: d 176 MET cc_start: 0.6950 (mtm) cc_final: 0.6418 (ptp) REVERT: d 189 TYR cc_start: 0.6285 (t80) cc_final: 0.5900 (t80) REVERT: d 261 TYR cc_start: 0.5601 (t80) cc_final: 0.5360 (t80) REVERT: d 276 LEU cc_start: 0.6742 (pp) cc_final: 0.6333 (pp) REVERT: d 294 PHE cc_start: 0.7777 (m-80) cc_final: 0.7359 (m-80) REVERT: d 324 GLN cc_start: 0.7900 (tp40) cc_final: 0.7131 (tp-100) REVERT: d 328 ASN cc_start: 0.7586 (m110) cc_final: 0.7274 (m110) REVERT: d 334 GLU cc_start: 0.4623 (mm-30) cc_final: 0.4299 (mm-30) REVERT: d 339 ARG cc_start: 0.5048 (mpp80) cc_final: 0.4716 (mpp80) REVERT: d 346 ASN cc_start: 0.6965 (t0) cc_final: 0.6706 (t0) REVERT: a 53 ASN cc_start: 0.8004 (m-40) cc_final: 0.7722 (p0) REVERT: a 60 GLU cc_start: 0.7948 (tp30) cc_final: 0.7642 (mm-30) REVERT: a 284 ASP cc_start: 0.7338 (m-30) cc_final: 0.7032 (m-30) REVERT: a 285 HIS cc_start: 0.5939 (t70) cc_final: 0.5379 (t70) REVERT: a 288 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7456 (ttp-170) REVERT: a 329 GLU cc_start: 0.7556 (tt0) cc_final: 0.6718 (mp0) REVERT: a 470 ILE cc_start: 0.7050 (mt) cc_final: 0.6814 (mt) REVERT: a 486 TRP cc_start: 0.4253 (m100) cc_final: 0.3898 (m100) REVERT: a 544 LYS cc_start: 0.7813 (mttt) cc_final: 0.7565 (ptpt) REVERT: a 546 LYS cc_start: 0.8308 (mttt) cc_final: 0.7970 (ptpt) REVERT: a 565 PHE cc_start: 0.7229 (m-80) cc_final: 0.6801 (m-80) REVERT: a 610 SER cc_start: 0.7934 (t) cc_final: 0.7550 (m) REVERT: a 623 MET cc_start: 0.8597 (ttp) cc_final: 0.8044 (tpt) REVERT: a 722 GLN cc_start: 0.8048 (tp40) cc_final: 0.7741 (tp40) REVERT: a 740 TYR cc_start: 0.8266 (m-80) cc_final: 0.7744 (m-80) REVERT: a 769 ARG cc_start: 0.5753 (mtm180) cc_final: 0.5064 (mmt180) REVERT: e 40 MET cc_start: 0.6145 (tmm) cc_final: 0.5791 (tmm) REVERT: e 77 ARG cc_start: 0.4551 (mtp180) cc_final: 0.4163 (tpm170) REVERT: f 29 LEU cc_start: 0.8429 (tp) cc_final: 0.8182 (tp) REVERT: f 63 GLU cc_start: 0.6859 (tp30) cc_final: 0.6235 (tt0) REVERT: c 377 LEU cc_start: 0.7372 (mp) cc_final: 0.7066 (pp) REVERT: c 381 ASN cc_start: 0.6772 (t0) cc_final: 0.6055 (p0) REVERT: c 388 MET cc_start: 0.5854 (tpp) cc_final: 0.5059 (mmt) REVERT: c 429 MET cc_start: 0.7731 (mmm) cc_final: 0.7512 (mmm) outliers start: 30 outliers final: 10 residues processed: 2247 average time/residue: 0.5908 time to fit residues: 2257.5452 Evaluate side-chains 1757 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1743 time to evaluate : 5.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 701 optimal weight: 0.9980 chunk 629 optimal weight: 9.9990 chunk 349 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 651 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 484 optimal weight: 0.0020 chunk 754 optimal weight: 7.9990 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 92 GLN 1 112 GLN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 522 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 5 209 GLN 5 350 GLN 5 482 GLN 7 16 GLN 8 14 HIS 9 126 GLN Q 77 ASN R 113 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 GLN U 102 GLN U 324 GLN U 451 ASN d 13 ASN d 84 HIS d 183 ASN a 114 ASN a 494 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 376 ASN ** c 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 66820 Z= 0.205 Angle : 0.605 10.575 90305 Z= 0.318 Chirality : 0.042 0.244 10236 Planarity : 0.004 0.114 11580 Dihedral : 4.596 83.021 9108 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 0.23 % Allowed : 3.64 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 8319 helix: 1.55 (0.08), residues: 4675 sheet: -0.43 (0.20), residues: 688 loop : -1.39 (0.12), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 16 HIS 0.006 0.001 HIS 8 14 PHE 0.049 0.002 PHE e 51 TYR 0.040 0.002 TYR o 144 ARG 0.015 0.001 ARG 7 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2068 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2052 time to evaluate : 5.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 89 LYS cc_start: 0.7340 (tttt) cc_final: 0.6551 (tppt) REVERT: b 146 LEU cc_start: 0.7711 (mm) cc_final: 0.7243 (tp) REVERT: b 150 PHE cc_start: 0.8308 (m-80) cc_final: 0.8061 (m-80) REVERT: g 61 MET cc_start: 0.8483 (mmm) cc_final: 0.8125 (mmm) REVERT: h 28 MET cc_start: 0.7044 (mmm) cc_final: 0.6627 (mmm) REVERT: h 44 MET cc_start: 0.7334 (tmm) cc_final: 0.7016 (ppp) REVERT: h 57 ILE cc_start: 0.7423 (mm) cc_final: 0.6986 (mm) REVERT: h 61 MET cc_start: 0.8296 (mtp) cc_final: 0.7843 (mmm) REVERT: h 131 MET cc_start: 0.7322 (ttp) cc_final: 0.7011 (ttp) REVERT: h 132 ILE cc_start: 0.6892 (mm) cc_final: 0.6682 (mm) REVERT: h 144 TYR cc_start: 0.8394 (m-10) cc_final: 0.8107 (m-10) REVERT: h 153 SER cc_start: 0.7944 (m) cc_final: 0.7734 (p) REVERT: i 61 MET cc_start: 0.6889 (mmm) cc_final: 0.6609 (mmt) REVERT: i 82 ASP cc_start: 0.6754 (m-30) cc_final: 0.6213 (t70) REVERT: i 84 ILE cc_start: 0.5519 (tt) cc_final: 0.5190 (pt) REVERT: i 131 MET cc_start: 0.6478 (ttp) cc_final: 0.6060 (ppp) REVERT: i 155 LYS cc_start: 0.5716 (mmtt) cc_final: 0.5308 (mmmt) REVERT: j 28 MET cc_start: 0.8822 (mtp) cc_final: 0.8560 (mtp) REVERT: j 51 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7001 (tt) REVERT: j 84 ILE cc_start: 0.7084 (mt) cc_final: 0.6798 (mm) REVERT: j 112 ILE cc_start: 0.5583 (tp) cc_final: 0.5283 (tp) REVERT: k 98 SER cc_start: 0.3580 (p) cc_final: 0.3212 (p) REVERT: l 14 PHE cc_start: 0.7395 (m-80) cc_final: 0.7027 (m-80) REVERT: l 53 MET cc_start: 0.7890 (mmm) cc_final: 0.6330 (tmm) REVERT: l 92 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6922 (mp10) REVERT: l 131 MET cc_start: 0.7453 (ttp) cc_final: 0.7075 (ttp) REVERT: l 132 ILE cc_start: 0.6722 (mm) cc_final: 0.6017 (mt) REVERT: m 14 PHE cc_start: 0.7350 (m-80) cc_final: 0.7104 (m-80) REVERT: n 61 MET cc_start: 0.6786 (mmm) cc_final: 0.6512 (mmm) REVERT: n 82 ASP cc_start: 0.7355 (m-30) cc_final: 0.4426 (m-30) REVERT: n 123 GLN cc_start: 0.6231 (mm110) cc_final: 0.6023 (mm110) REVERT: n 134 ILE cc_start: 0.6742 (tp) cc_final: 0.6181 (tp) REVERT: o 48 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6448 (mpt180) REVERT: o 54 LYS cc_start: 0.6168 (tptt) cc_final: 0.5101 (tttt) REVERT: o 127 LEU cc_start: 0.7077 (mm) cc_final: 0.6532 (tp) REVERT: o 144 TYR cc_start: 0.8095 (m-80) cc_final: 0.7761 (m-80) REVERT: o 148 VAL cc_start: 0.5279 (t) cc_final: 0.4968 (t) REVERT: 1 86 LEU cc_start: 0.8522 (tp) cc_final: 0.7527 (tp) REVERT: 1 233 VAL cc_start: 0.8083 (m) cc_final: 0.7761 (m) REVERT: 1 274 TYR cc_start: 0.8925 (t80) cc_final: 0.8276 (t80) REVERT: 1 279 GLU cc_start: 0.7472 (pm20) cc_final: 0.5670 (mm-30) REVERT: 1 286 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7477 (mm-30) REVERT: 1 299 ASP cc_start: 0.5750 (p0) cc_final: 0.5046 (m-30) REVERT: 1 324 GLU cc_start: 0.8515 (tt0) cc_final: 0.7735 (tt0) REVERT: 1 328 TYR cc_start: 0.7829 (m-10) cc_final: 0.7289 (m-80) REVERT: 1 346 MET cc_start: 0.7907 (ttt) cc_final: 0.7579 (ttt) REVERT: 1 404 VAL cc_start: 0.9377 (t) cc_final: 0.9172 (p) REVERT: 1 494 GLN cc_start: 0.7524 (tm-30) cc_final: 0.6973 (tp40) REVERT: 1 508 THR cc_start: 0.6337 (m) cc_final: 0.5963 (p) REVERT: 1 522 GLN cc_start: 0.7903 (tt0) cc_final: 0.7501 (tt0) REVERT: 1 574 MET cc_start: 0.5038 (ptm) cc_final: 0.4751 (mpp) REVERT: 1 600 ASP cc_start: 0.8900 (m-30) cc_final: 0.8653 (m-30) REVERT: 0 227 LEU cc_start: 0.8687 (tp) cc_final: 0.8415 (tp) REVERT: 0 356 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6862 (tm-30) REVERT: 0 411 SER cc_start: 0.8639 (t) cc_final: 0.8428 (t) REVERT: 0 445 PHE cc_start: 0.6875 (p90) cc_final: 0.5493 (m-80) REVERT: 0 456 LYS cc_start: 0.8453 (mmpt) cc_final: 0.7972 (mtmt) REVERT: 2 34 MET cc_start: 0.7268 (tmm) cc_final: 0.6906 (tmm) REVERT: 2 55 ILE cc_start: 0.8203 (mm) cc_final: 0.6979 (mm) REVERT: 2 113 THR cc_start: 0.8730 (p) cc_final: 0.8198 (t) REVERT: 2 282 ASN cc_start: 0.8004 (t0) cc_final: 0.7776 (t0) REVERT: 2 335 GLU cc_start: 0.6744 (mt-10) cc_final: 0.6517 (mt-10) REVERT: 2 387 GLU cc_start: 0.6287 (tp30) cc_final: 0.5771 (tp30) REVERT: 2 388 ARG cc_start: 0.7457 (mmm-85) cc_final: 0.7048 (mmm-85) REVERT: 2 463 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7789 (tm-30) REVERT: 3 70 GLU cc_start: 0.7709 (pt0) cc_final: 0.7240 (pt0) REVERT: 3 87 LEU cc_start: 0.8979 (mt) cc_final: 0.8470 (mt) REVERT: 3 97 GLN cc_start: 0.9211 (pt0) cc_final: 0.8799 (pt0) REVERT: 3 127 MET cc_start: 0.8080 (mtp) cc_final: 0.7647 (mtp) REVERT: 3 202 ILE cc_start: 0.8976 (mt) cc_final: 0.8762 (mt) REVERT: 3 205 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7323 (tm-30) REVERT: 3 206 ILE cc_start: 0.8864 (mt) cc_final: 0.8584 (mt) REVERT: 3 326 TYR cc_start: 0.7999 (p90) cc_final: 0.7698 (p90) REVERT: 3 361 ILE cc_start: 0.7284 (tp) cc_final: 0.6795 (tt) REVERT: 3 374 GLU cc_start: 0.8633 (pm20) cc_final: 0.8084 (pm20) REVERT: 3 392 ILE cc_start: 0.8357 (mt) cc_final: 0.7991 (mt) REVERT: 3 394 VAL cc_start: 0.9115 (m) cc_final: 0.8876 (p) REVERT: 3 423 TYR cc_start: 0.8633 (m-80) cc_final: 0.8386 (m-80) REVERT: 3 491 MET cc_start: 0.6170 (mtt) cc_final: 0.5618 (ppp) REVERT: 4 70 GLU cc_start: 0.7802 (pt0) cc_final: 0.7153 (pt0) REVERT: 4 97 GLN cc_start: 0.7635 (pt0) cc_final: 0.7212 (pt0) REVERT: 4 152 ASP cc_start: 0.7799 (t0) cc_final: 0.7400 (p0) REVERT: 4 207 CYS cc_start: 0.7227 (t) cc_final: 0.7003 (t) REVERT: 4 271 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8500 (mtp85) REVERT: 4 290 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6715 (pt0) REVERT: 5 61 ASP cc_start: 0.8175 (p0) cc_final: 0.7971 (p0) REVERT: 5 119 LEU cc_start: 0.8769 (tp) cc_final: 0.8532 (tp) REVERT: 5 245 LYS cc_start: 0.8320 (ttpt) cc_final: 0.8114 (tmmt) REVERT: 5 311 SER cc_start: 0.8460 (t) cc_final: 0.8147 (t) REVERT: 5 382 GLN cc_start: 0.7934 (mp10) cc_final: 0.7706 (mp10) REVERT: 5 393 ASN cc_start: 0.8032 (t0) cc_final: 0.6575 (t0) REVERT: 5 423 TYR cc_start: 0.8101 (t80) cc_final: 0.7890 (t80) REVERT: 5 485 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7049 (mmm160) REVERT: 7 23 LEU cc_start: 0.7753 (tp) cc_final: 0.7473 (tp) REVERT: 7 163 LYS cc_start: 0.8459 (mmpt) cc_final: 0.7702 (mtpt) REVERT: 7 168 ARG cc_start: 0.5789 (ttt180) cc_final: 0.5547 (ttt180) REVERT: 8 44 ARG cc_start: 0.6639 (mtp180) cc_final: 0.6242 (mtt90) REVERT: 8 54 MET cc_start: 0.7523 (mpp) cc_final: 0.7149 (mpp) REVERT: 8 59 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7386 (mmmm) REVERT: 8 72 MET cc_start: 0.8032 (mtm) cc_final: 0.7573 (tpt) REVERT: 8 208 MET cc_start: 0.6907 (tmm) cc_final: 0.6558 (tmm) REVERT: 9 54 MET cc_start: 0.7530 (mmt) cc_final: 0.6966 (mmt) REVERT: 9 154 MET cc_start: 0.8213 (mmp) cc_final: 0.7783 (mmm) REVERT: 9 191 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8776 (ttpt) REVERT: 9 197 GLU cc_start: 0.8312 (mp0) cc_final: 0.7909 (mp0) REVERT: Q 67 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7784 (tm-30) REVERT: Q 201 ASP cc_start: 0.8713 (t0) cc_final: 0.8506 (t70) REVERT: R 28 ARG cc_start: 0.4419 (ttt180) cc_final: 0.4173 (ttt180) REVERT: R 45 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6152 (tm-30) REVERT: R 58 LYS cc_start: 0.6298 (mttt) cc_final: 0.6029 (mmmt) REVERT: T 16 LYS cc_start: 0.8148 (mttt) cc_final: 0.7022 (tttp) REVERT: T 34 LYS cc_start: 0.8280 (tppt) cc_final: 0.7517 (mttt) REVERT: V 47 TYR cc_start: 0.5916 (m-10) cc_final: 0.5636 (m-10) REVERT: X 51 THR cc_start: 0.8021 (m) cc_final: 0.7613 (t) REVERT: X 55 PHE cc_start: 0.7134 (m-80) cc_final: 0.6772 (m-80) REVERT: 6 66 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7250 (mt-10) REVERT: 6 82 ASP cc_start: 0.5479 (t0) cc_final: 0.5004 (m-30) REVERT: 6 109 MET cc_start: 0.7512 (tmm) cc_final: 0.6236 (mtm) REVERT: 6 298 LYS cc_start: 0.6859 (mmtt) cc_final: 0.6556 (mtmt) REVERT: 6 301 ARG cc_start: 0.7207 (mtp180) cc_final: 0.6865 (mmm-85) REVERT: 6 338 LEU cc_start: 0.6494 (mt) cc_final: 0.5957 (mt) REVERT: 6 341 HIS cc_start: 0.6713 (p90) cc_final: 0.5914 (m90) REVERT: U 65 MET cc_start: 0.6759 (ppp) cc_final: 0.6297 (ppp) REVERT: U 96 MET cc_start: 0.1311 (ptm) cc_final: 0.0366 (mmt) REVERT: U 127 LEU cc_start: 0.6053 (mt) cc_final: 0.5780 (pt) REVERT: U 147 LYS cc_start: 0.6131 (mmmm) cc_final: 0.5696 (tptt) REVERT: U 156 MET cc_start: 0.6813 (ptm) cc_final: 0.6432 (ptt) REVERT: U 163 TYR cc_start: 0.6955 (t80) cc_final: 0.6561 (t80) REVERT: U 165 PHE cc_start: 0.7301 (m-80) cc_final: 0.7054 (m-80) REVERT: U 234 LYS cc_start: 0.6028 (tttt) cc_final: 0.5564 (mptt) REVERT: U 256 MET cc_start: 0.6074 (mmm) cc_final: 0.5791 (mmm) REVERT: U 321 LEU cc_start: 0.8078 (mm) cc_final: 0.7722 (mt) REVERT: U 324 GLN cc_start: 0.6947 (mp10) cc_final: 0.6579 (mp-120) REVERT: U 383 LEU cc_start: 0.7181 (mt) cc_final: 0.6135 (mt) REVERT: U 434 LYS cc_start: 0.5905 (pttm) cc_final: 0.5357 (tttp) REVERT: U 440 HIS cc_start: 0.6092 (m-70) cc_final: 0.5497 (m170) REVERT: d 38 GLN cc_start: 0.6201 (mm-40) cc_final: 0.5261 (mt0) REVERT: d 85 MET cc_start: 0.7968 (tmm) cc_final: 0.7664 (tmm) REVERT: d 128 LYS cc_start: 0.8625 (mmpt) cc_final: 0.8319 (mptt) REVERT: d 176 MET cc_start: 0.6702 (mtm) cc_final: 0.6220 (ptp) REVERT: d 189 TYR cc_start: 0.6669 (t80) cc_final: 0.6234 (t80) REVERT: d 262 GLU cc_start: 0.6518 (tp30) cc_final: 0.5597 (mt-10) REVERT: d 339 ARG cc_start: 0.4659 (mpp80) cc_final: 0.4458 (mpp80) REVERT: d 346 ASN cc_start: 0.7230 (t0) cc_final: 0.6973 (t0) REVERT: a 53 ASN cc_start: 0.7932 (m-40) cc_final: 0.7675 (p0) REVERT: a 60 GLU cc_start: 0.7850 (tp30) cc_final: 0.7589 (mm-30) REVERT: a 129 LYS cc_start: 0.7326 (pttp) cc_final: 0.7062 (pttp) REVERT: a 288 ARG cc_start: 0.8070 (ptt180) cc_final: 0.7867 (ptm160) REVERT: a 290 LEU cc_start: 0.8018 (mt) cc_final: 0.7573 (tt) REVERT: a 316 LEU cc_start: 0.8131 (mm) cc_final: 0.7904 (tp) REVERT: a 329 GLU cc_start: 0.7384 (tt0) cc_final: 0.6553 (mp0) REVERT: a 383 ASN cc_start: 0.8789 (t0) cc_final: 0.8309 (m-40) REVERT: a 470 ILE cc_start: 0.7091 (mt) cc_final: 0.6874 (mt) REVERT: a 486 TRP cc_start: 0.4368 (m100) cc_final: 0.4141 (m100) REVERT: a 565 PHE cc_start: 0.7321 (m-80) cc_final: 0.6772 (m-80) REVERT: a 623 MET cc_start: 0.8536 (ttp) cc_final: 0.8040 (tpt) REVERT: a 736 ASN cc_start: 0.7736 (m-40) cc_final: 0.7505 (m-40) REVERT: a 740 TYR cc_start: 0.8407 (m-80) cc_final: 0.7774 (m-80) REVERT: a 769 ARG cc_start: 0.5690 (mtm180) cc_final: 0.5019 (mmt180) REVERT: e 40 MET cc_start: 0.6378 (tmm) cc_final: 0.5939 (tmm) REVERT: e 77 ARG cc_start: 0.4672 (mtp180) cc_final: 0.4120 (mmm160) REVERT: f 63 GLU cc_start: 0.6784 (tp30) cc_final: 0.6270 (tt0) REVERT: c 421 MET cc_start: 0.6408 (mpp) cc_final: 0.5979 (ptt) outliers start: 16 outliers final: 5 residues processed: 2059 average time/residue: 0.5966 time to fit residues: 2102.4940 Evaluate side-chains 1714 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1708 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 419 optimal weight: 5.9990 chunk 234 optimal weight: 0.1980 chunk 628 optimal weight: 0.5980 chunk 513 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 755 optimal weight: 0.9980 chunk 816 optimal weight: 6.9990 chunk 673 optimal weight: 0.0470 chunk 749 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 606 optimal weight: 0.0040 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: k 123 GLN n 124 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 242 GLN 0 522 GLN 3 251 ASN 4 156 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 206 GLN 9 113 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 296 HIS U 17 ASN U 259 HIS a 114 ASN a 494 GLN a 669 GLN ** a 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 90 ASN c 392 ASN c 394 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 66820 Z= 0.166 Angle : 0.565 10.049 90305 Z= 0.294 Chirality : 0.041 0.199 10236 Planarity : 0.004 0.149 11580 Dihedral : 4.368 81.162 9108 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8319 helix: 1.73 (0.08), residues: 4696 sheet: -0.03 (0.20), residues: 681 loop : -1.33 (0.12), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 67 HIS 0.008 0.001 HIS U 259 PHE 0.039 0.002 PHE c 433 TYR 0.030 0.001 TYR i 68 ARG 0.010 0.000 ARG j 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2081 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2070 time to evaluate : 5.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.9074 (pt) cc_final: 0.8750 (tp) REVERT: b 89 LYS cc_start: 0.7308 (tttt) cc_final: 0.6729 (tppt) REVERT: b 146 LEU cc_start: 0.8292 (mm) cc_final: 0.7651 (tp) REVERT: g 61 MET cc_start: 0.8319 (mmm) cc_final: 0.8018 (mmm) REVERT: h 28 MET cc_start: 0.7086 (mmm) cc_final: 0.6728 (mmp) REVERT: h 50 GLU cc_start: 0.5710 (mt-10) cc_final: 0.5270 (tm-30) REVERT: h 57 ILE cc_start: 0.7374 (mm) cc_final: 0.6882 (mm) REVERT: h 61 MET cc_start: 0.8305 (mtp) cc_final: 0.7726 (mmm) REVERT: h 144 TYR cc_start: 0.8373 (m-10) cc_final: 0.8084 (m-10) REVERT: i 56 ILE cc_start: 0.5950 (pt) cc_final: 0.5650 (tt) REVERT: i 61 MET cc_start: 0.6787 (mmm) cc_final: 0.6482 (mmt) REVERT: i 68 TYR cc_start: 0.7982 (m-80) cc_final: 0.7771 (m-80) REVERT: i 82 ASP cc_start: 0.7099 (m-30) cc_final: 0.6257 (t70) REVERT: i 84 ILE cc_start: 0.5499 (tt) cc_final: 0.5158 (pt) REVERT: i 131 MET cc_start: 0.6338 (ttp) cc_final: 0.6028 (ppp) REVERT: i 155 LYS cc_start: 0.5692 (mmtt) cc_final: 0.5359 (mmmt) REVERT: j 28 MET cc_start: 0.8806 (mtp) cc_final: 0.8470 (mtp) REVERT: j 51 LEU cc_start: 0.8201 (pp) cc_final: 0.7027 (tt) REVERT: j 84 ILE cc_start: 0.6930 (mt) cc_final: 0.6683 (mm) REVERT: l 14 PHE cc_start: 0.7344 (m-80) cc_final: 0.6919 (m-80) REVERT: l 44 MET cc_start: 0.6803 (tpp) cc_final: 0.5945 (mmt) REVERT: l 53 MET cc_start: 0.7972 (mmm) cc_final: 0.7070 (ptt) REVERT: l 92 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7065 (mm-40) REVERT: l 131 MET cc_start: 0.7346 (ttp) cc_final: 0.6859 (ttp) REVERT: m 14 PHE cc_start: 0.7574 (m-80) cc_final: 0.7246 (m-80) REVERT: n 24 VAL cc_start: 0.6551 (m) cc_final: 0.6311 (m) REVERT: n 61 MET cc_start: 0.6894 (mmm) cc_final: 0.6516 (mmm) REVERT: n 82 ASP cc_start: 0.7341 (m-30) cc_final: 0.4355 (m-30) REVERT: n 86 LEU cc_start: 0.7351 (tp) cc_final: 0.7052 (tp) REVERT: n 127 LEU cc_start: 0.6846 (mm) cc_final: 0.6244 (pt) REVERT: n 134 ILE cc_start: 0.6590 (tp) cc_final: 0.6052 (tp) REVERT: o 48 ARG cc_start: 0.6978 (mmm-85) cc_final: 0.6013 (mpt180) REVERT: o 54 LYS cc_start: 0.6369 (tptt) cc_final: 0.5282 (tttt) REVERT: o 70 LEU cc_start: 0.8549 (mt) cc_final: 0.7975 (mt) REVERT: o 127 LEU cc_start: 0.7264 (mm) cc_final: 0.6608 (tp) REVERT: o 144 TYR cc_start: 0.8005 (m-10) cc_final: 0.7777 (m-80) REVERT: o 148 VAL cc_start: 0.5289 (t) cc_final: 0.5006 (t) REVERT: 1 67 TYR cc_start: 0.8067 (m-80) cc_final: 0.7715 (m-80) REVERT: 1 86 LEU cc_start: 0.8183 (tp) cc_final: 0.7621 (tp) REVERT: 1 242 GLN cc_start: 0.7580 (tt0) cc_final: 0.7192 (tt0) REVERT: 1 262 SER cc_start: 0.9093 (m) cc_final: 0.8868 (t) REVERT: 1 279 GLU cc_start: 0.7521 (pm20) cc_final: 0.5493 (mm-30) REVERT: 1 299 ASP cc_start: 0.5794 (p0) cc_final: 0.4976 (m-30) REVERT: 1 306 MET cc_start: 0.7651 (mmm) cc_final: 0.7317 (tpt) REVERT: 1 309 THR cc_start: 0.7640 (m) cc_final: 0.7358 (m) REVERT: 1 328 TYR cc_start: 0.7875 (m-10) cc_final: 0.7431 (m-80) REVERT: 1 508 THR cc_start: 0.6457 (m) cc_final: 0.6048 (p) REVERT: 1 550 MET cc_start: 0.7344 (mtp) cc_final: 0.6899 (mtp) REVERT: 1 600 ASP cc_start: 0.8903 (m-30) cc_final: 0.8681 (m-30) REVERT: 0 53 GLU cc_start: 0.8279 (tp30) cc_final: 0.7927 (tp30) REVERT: 0 356 GLU cc_start: 0.7682 (mt-10) cc_final: 0.6824 (tm-30) REVERT: 0 358 LEU cc_start: 0.9183 (mt) cc_final: 0.8922 (mt) REVERT: 0 377 TYR cc_start: 0.7775 (p90) cc_final: 0.7238 (p90) REVERT: 0 439 LEU cc_start: 0.6899 (mm) cc_final: 0.6377 (tt) REVERT: 0 445 PHE cc_start: 0.6843 (p90) cc_final: 0.5407 (m-80) REVERT: 0 456 LYS cc_start: 0.8506 (mmpt) cc_final: 0.7986 (mtmt) REVERT: 0 534 PHE cc_start: 0.4889 (t80) cc_final: 0.4467 (t80) REVERT: 0 572 GLU cc_start: 0.5925 (tm-30) cc_final: 0.5340 (mt-10) REVERT: 2 34 MET cc_start: 0.7416 (tmm) cc_final: 0.7038 (tmm) REVERT: 2 55 ILE cc_start: 0.8379 (mm) cc_final: 0.7327 (mm) REVERT: 2 113 THR cc_start: 0.8799 (p) cc_final: 0.8286 (t) REVERT: 2 207 GLN cc_start: 0.6276 (pm20) cc_final: 0.6061 (pm20) REVERT: 2 335 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6052 (mt-10) REVERT: 2 387 GLU cc_start: 0.6343 (tp30) cc_final: 0.5664 (tp30) REVERT: 2 388 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.6887 (mmm-85) REVERT: 3 70 GLU cc_start: 0.7488 (pt0) cc_final: 0.7008 (pt0) REVERT: 3 146 LEU cc_start: 0.8252 (tp) cc_final: 0.7838 (tp) REVERT: 3 205 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7270 (tm-30) REVERT: 3 337 ARG cc_start: 0.7388 (mtp85) cc_final: 0.7108 (mtp85) REVERT: 3 392 ILE cc_start: 0.8303 (mt) cc_final: 0.8020 (mt) REVERT: 3 491 MET cc_start: 0.5974 (mtt) cc_final: 0.5469 (ppp) REVERT: 4 70 GLU cc_start: 0.7734 (pt0) cc_final: 0.7047 (pt0) REVERT: 4 152 ASP cc_start: 0.7702 (t0) cc_final: 0.7270 (p0) REVERT: 4 164 ILE cc_start: 0.8355 (tp) cc_final: 0.7989 (tp) REVERT: 4 290 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6552 (pt0) REVERT: 4 299 ASP cc_start: 0.7624 (t0) cc_final: 0.7308 (t0) REVERT: 4 421 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8176 (mm-40) REVERT: 5 119 LEU cc_start: 0.8798 (tp) cc_final: 0.8507 (tp) REVERT: 5 148 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7885 (tm-30) REVERT: 5 244 PHE cc_start: 0.8217 (m-10) cc_final: 0.8000 (m-10) REVERT: 5 350 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7632 (tp-100) REVERT: 5 435 MET cc_start: 0.6697 (mtp) cc_final: 0.6428 (mtp) REVERT: 5 485 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6945 (mmm160) REVERT: 5 491 MET cc_start: 0.6374 (mtp) cc_final: 0.5921 (mtp) REVERT: 7 23 LEU cc_start: 0.7696 (tp) cc_final: 0.7314 (tp) REVERT: 7 71 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6693 (mt-10) REVERT: 7 97 LYS cc_start: 0.7202 (tttt) cc_final: 0.6382 (tptt) REVERT: 7 163 LYS cc_start: 0.8437 (mmpt) cc_final: 0.7672 (mtpt) REVERT: 7 170 ASN cc_start: 0.6177 (m-40) cc_final: 0.5839 (t0) REVERT: 7 196 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8317 (tmm-80) REVERT: 8 54 MET cc_start: 0.7658 (mpp) cc_final: 0.7301 (mpp) REVERT: 8 59 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7006 (pptt) REVERT: 8 72 MET cc_start: 0.8266 (mtm) cc_final: 0.7664 (tpt) REVERT: 8 185 ASN cc_start: 0.8846 (p0) cc_final: 0.8582 (p0) REVERT: 9 54 MET cc_start: 0.7380 (mmt) cc_final: 0.6978 (mmm) REVERT: 9 57 TYR cc_start: 0.6271 (t80) cc_final: 0.6007 (t80) REVERT: 9 154 MET cc_start: 0.8227 (mmp) cc_final: 0.7876 (mmm) REVERT: 9 197 GLU cc_start: 0.8340 (mp0) cc_final: 0.7718 (mp0) REVERT: 9 206 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8221 (mt0) REVERT: Q 125 TYR cc_start: 0.7726 (m-10) cc_final: 0.7438 (m-80) REVERT: Q 132 MET cc_start: 0.7040 (mtt) cc_final: 0.6300 (mtp) REVERT: Q 140 ASP cc_start: 0.7787 (m-30) cc_final: 0.7177 (t0) REVERT: Q 201 ASP cc_start: 0.8691 (t0) cc_final: 0.8481 (t70) REVERT: R 45 GLU cc_start: 0.7274 (mm-30) cc_final: 0.5976 (tm-30) REVERT: R 58 LYS cc_start: 0.6286 (mttt) cc_final: 0.5996 (mttm) REVERT: R 79 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8171 (ttp80) REVERT: R 96 LEU cc_start: 0.9058 (tp) cc_final: 0.8853 (tp) REVERT: T 16 LYS cc_start: 0.8019 (mttt) cc_final: 0.6874 (tttp) REVERT: T 34 LYS cc_start: 0.8314 (tppt) cc_final: 0.7672 (mttt) REVERT: V 47 TYR cc_start: 0.5731 (m-10) cc_final: 0.5448 (m-10) REVERT: X 27 GLU cc_start: 0.7421 (pp20) cc_final: 0.7206 (pp20) REVERT: X 51 THR cc_start: 0.8080 (m) cc_final: 0.7468 (t) REVERT: 6 66 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7200 (mt-10) REVERT: 6 82 ASP cc_start: 0.5523 (t0) cc_final: 0.5037 (m-30) REVERT: 6 109 MET cc_start: 0.7397 (tmm) cc_final: 0.6168 (mtm) REVERT: 6 298 LYS cc_start: 0.6800 (mmtt) cc_final: 0.6540 (mtmt) REVERT: 6 338 LEU cc_start: 0.6601 (mt) cc_final: 0.6127 (mt) REVERT: 6 341 HIS cc_start: 0.6838 (p90) cc_final: 0.5986 (m90) REVERT: U 65 MET cc_start: 0.6592 (ppp) cc_final: 0.6232 (ppp) REVERT: U 96 MET cc_start: 0.1320 (ptm) cc_final: 0.0404 (mmt) REVERT: U 147 LYS cc_start: 0.6075 (mmmm) cc_final: 0.5602 (tptt) REVERT: U 156 MET cc_start: 0.6747 (ptm) cc_final: 0.6392 (ptt) REVERT: U 163 TYR cc_start: 0.6946 (t80) cc_final: 0.6544 (t80) REVERT: U 165 PHE cc_start: 0.7449 (m-80) cc_final: 0.7037 (m-80) REVERT: U 234 LYS cc_start: 0.6181 (tttt) cc_final: 0.5695 (mptt) REVERT: U 256 MET cc_start: 0.5920 (mmm) cc_final: 0.5670 (mmm) REVERT: U 320 ASN cc_start: 0.8187 (t0) cc_final: 0.7819 (t0) REVERT: U 321 LEU cc_start: 0.8106 (mm) cc_final: 0.7868 (mt) REVERT: U 324 GLN cc_start: 0.7104 (mp10) cc_final: 0.6654 (mp-120) REVERT: U 383 LEU cc_start: 0.7130 (mt) cc_final: 0.6028 (mt) REVERT: U 434 LYS cc_start: 0.5923 (pttm) cc_final: 0.5401 (tttp) REVERT: d 38 GLN cc_start: 0.6244 (mm-40) cc_final: 0.5352 (mt0) REVERT: d 71 ASP cc_start: 0.7573 (t70) cc_final: 0.7373 (t70) REVERT: d 75 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7839 (mmmt) REVERT: d 85 MET cc_start: 0.7720 (tmm) cc_final: 0.7296 (tmm) REVERT: d 128 LYS cc_start: 0.8632 (mmpt) cc_final: 0.8216 (mtpt) REVERT: d 189 TYR cc_start: 0.6660 (t80) cc_final: 0.6167 (t80) REVERT: d 262 GLU cc_start: 0.6495 (tp30) cc_final: 0.5654 (mt-10) REVERT: d 328 ASN cc_start: 0.7306 (m110) cc_final: 0.7091 (m-40) REVERT: d 346 ASN cc_start: 0.7054 (t0) cc_final: 0.6688 (t0) REVERT: d 349 PRO cc_start: 0.7534 (Cg_endo) cc_final: 0.7180 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8472 (tptm) cc_final: 0.8134 (tptp) REVERT: a 66 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7822 (mmt-90) REVERT: a 290 LEU cc_start: 0.8039 (mt) cc_final: 0.7451 (tt) REVERT: a 329 GLU cc_start: 0.7403 (tt0) cc_final: 0.6521 (mp0) REVERT: a 345 ARG cc_start: 0.7093 (ptt90) cc_final: 0.6578 (mmt180) REVERT: a 383 ASN cc_start: 0.8772 (t0) cc_final: 0.8350 (m-40) REVERT: a 470 ILE cc_start: 0.7009 (mt) cc_final: 0.6790 (mt) REVERT: a 546 LYS cc_start: 0.8223 (mttt) cc_final: 0.7896 (ptpt) REVERT: a 565 PHE cc_start: 0.7314 (m-80) cc_final: 0.6932 (m-80) REVERT: a 623 MET cc_start: 0.8522 (ttp) cc_final: 0.7997 (tpt) REVERT: a 740 TYR cc_start: 0.8460 (m-80) cc_final: 0.7767 (m-80) REVERT: a 769 ARG cc_start: 0.5663 (mtm180) cc_final: 0.4936 (mmt180) REVERT: a 831 HIS cc_start: 0.6462 (p90) cc_final: 0.6026 (p-80) REVERT: e 12 ILE cc_start: 0.6661 (pt) cc_final: 0.6215 (pt) REVERT: e 40 MET cc_start: 0.6345 (tmm) cc_final: 0.6123 (ptp) REVERT: e 57 LEU cc_start: 0.7936 (mt) cc_final: 0.7607 (mt) REVERT: f 29 LEU cc_start: 0.8406 (tp) cc_final: 0.8147 (tp) REVERT: f 63 GLU cc_start: 0.6951 (tp30) cc_final: 0.6344 (tt0) REVERT: c 332 TYR cc_start: 0.5172 (m-80) cc_final: 0.4794 (m-80) REVERT: c 376 ASN cc_start: 0.7682 (m110) cc_final: 0.7387 (m110) REVERT: c 389 THR cc_start: 0.5003 (t) cc_final: 0.4798 (t) REVERT: c 392 ASN cc_start: 0.7414 (t0) cc_final: 0.6751 (t0) REVERT: c 425 THR cc_start: 0.9271 (m) cc_final: 0.9035 (m) REVERT: c 429 MET cc_start: 0.7757 (mmm) cc_final: 0.7306 (mmm) outliers start: 11 outliers final: 3 residues processed: 2076 average time/residue: 0.6198 time to fit residues: 2214.2590 Evaluate side-chains 1710 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1707 time to evaluate : 5.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 746 optimal weight: 5.9990 chunk 568 optimal weight: 4.9990 chunk 392 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 360 optimal weight: 0.0980 chunk 507 optimal weight: 6.9990 chunk 758 optimal weight: 3.9990 chunk 803 optimal weight: 7.9990 chunk 396 optimal weight: 7.9990 chunk 719 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN h 124 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 484 GLN 2 343 HIS 3 97 GLN 4 156 GLN 5 62 HIS 5 482 GLN 8 11 GLN 9 126 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 59 GLN ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 252 GLN U 17 ASN U 259 HIS d 88 HIS d 165 GLN a 76 ASN a 114 ASN ** a 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 66820 Z= 0.207 Angle : 0.584 12.001 90305 Z= 0.304 Chirality : 0.041 0.253 10236 Planarity : 0.004 0.138 11580 Dihedral : 4.386 78.995 9108 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.09), residues: 8319 helix: 1.77 (0.08), residues: 4672 sheet: -0.01 (0.20), residues: 711 loop : -1.32 (0.12), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 486 HIS 0.019 0.001 HIS a 350 PHE 0.070 0.002 PHE c 433 TYR 0.028 0.002 TYR g 68 ARG 0.010 0.001 ARG a 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1993 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1988 time to evaluate : 5.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8999 (pt) cc_final: 0.8717 (tp) REVERT: b 82 LYS cc_start: 0.7763 (tppt) cc_final: 0.7196 (tppt) REVERT: b 114 MET cc_start: 0.7834 (ttm) cc_final: 0.7617 (ttm) REVERT: b 146 LEU cc_start: 0.8625 (mm) cc_final: 0.7924 (mt) REVERT: b 168 GLN cc_start: 0.6935 (pp30) cc_final: 0.6699 (pp30) REVERT: g 61 MET cc_start: 0.8163 (mmm) cc_final: 0.7906 (mmm) REVERT: g 89 SER cc_start: 0.6716 (p) cc_final: 0.4954 (t) REVERT: h 28 MET cc_start: 0.6897 (mmm) cc_final: 0.6593 (mmp) REVERT: h 57 ILE cc_start: 0.7502 (mm) cc_final: 0.6983 (mm) REVERT: h 61 MET cc_start: 0.8356 (mtp) cc_final: 0.7834 (mmm) REVERT: h 144 TYR cc_start: 0.8455 (m-10) cc_final: 0.8167 (m-10) REVERT: i 61 MET cc_start: 0.6759 (mmm) cc_final: 0.6505 (mmt) REVERT: i 68 TYR cc_start: 0.8035 (m-80) cc_final: 0.7694 (m-80) REVERT: i 82 ASP cc_start: 0.7280 (m-30) cc_final: 0.6416 (t0) REVERT: i 84 ILE cc_start: 0.5501 (tt) cc_final: 0.5112 (pt) REVERT: i 131 MET cc_start: 0.6502 (ttp) cc_final: 0.6170 (ppp) REVERT: i 155 LYS cc_start: 0.5761 (mmtt) cc_final: 0.5408 (mmmt) REVERT: j 28 MET cc_start: 0.8825 (mtp) cc_final: 0.8523 (mtp) REVERT: j 51 LEU cc_start: 0.8264 (pp) cc_final: 0.7182 (tt) REVERT: l 53 MET cc_start: 0.8044 (mmm) cc_final: 0.6490 (tmm) REVERT: l 61 MET cc_start: 0.1648 (mtp) cc_final: 0.1247 (mtp) REVERT: l 131 MET cc_start: 0.7311 (ttp) cc_final: 0.6879 (ttp) REVERT: n 24 VAL cc_start: 0.6424 (m) cc_final: 0.6193 (m) REVERT: n 61 MET cc_start: 0.6751 (mmm) cc_final: 0.6304 (mmm) REVERT: n 70 LEU cc_start: 0.7396 (mt) cc_final: 0.7138 (mt) REVERT: n 82 ASP cc_start: 0.7361 (m-30) cc_final: 0.4424 (m-30) REVERT: n 86 LEU cc_start: 0.7375 (tp) cc_final: 0.7088 (tp) REVERT: n 123 GLN cc_start: 0.6399 (mm110) cc_final: 0.6117 (mm110) REVERT: o 54 LYS cc_start: 0.6584 (tptt) cc_final: 0.5499 (tttt) REVERT: o 70 LEU cc_start: 0.8866 (mt) cc_final: 0.8426 (mt) REVERT: 1 219 GLU cc_start: 0.9096 (pm20) cc_final: 0.8747 (pm20) REVERT: 1 232 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.6795 (mtm180) REVERT: 1 242 GLN cc_start: 0.7686 (tt0) cc_final: 0.7314 (tt0) REVERT: 1 279 GLU cc_start: 0.7210 (pm20) cc_final: 0.5629 (mm-30) REVERT: 1 306 MET cc_start: 0.7843 (mmm) cc_final: 0.7475 (tpt) REVERT: 1 311 LEU cc_start: 0.9153 (mt) cc_final: 0.8948 (mt) REVERT: 1 324 GLU cc_start: 0.8565 (tt0) cc_final: 0.7634 (tt0) REVERT: 1 328 TYR cc_start: 0.7952 (m-10) cc_final: 0.7392 (m-80) REVERT: 1 508 THR cc_start: 0.6228 (m) cc_final: 0.5911 (p) REVERT: 1 522 GLN cc_start: 0.7841 (tt0) cc_final: 0.7570 (tt0) REVERT: 1 541 LEU cc_start: 0.8648 (tt) cc_final: 0.8381 (tt) REVERT: 0 314 ASN cc_start: 0.8492 (t0) cc_final: 0.8101 (t0) REVERT: 0 347 MET cc_start: 0.7953 (mmt) cc_final: 0.7742 (mmt) REVERT: 0 356 GLU cc_start: 0.7894 (mt-10) cc_final: 0.6993 (tm-30) REVERT: 0 358 LEU cc_start: 0.9284 (mt) cc_final: 0.9076 (mt) REVERT: 0 394 CYS cc_start: 0.8679 (m) cc_final: 0.8455 (t) REVERT: 0 430 GLN cc_start: 0.7203 (tt0) cc_final: 0.6874 (tt0) REVERT: 0 445 PHE cc_start: 0.6773 (p90) cc_final: 0.5554 (m-10) REVERT: 0 456 LYS cc_start: 0.8569 (mmpt) cc_final: 0.7867 (mtmt) REVERT: 0 531 PHE cc_start: 0.6002 (t80) cc_final: 0.5139 (t80) REVERT: 0 572 GLU cc_start: 0.5875 (tm-30) cc_final: 0.5090 (mt-10) REVERT: 2 34 MET cc_start: 0.7399 (tmm) cc_final: 0.6967 (tmm) REVERT: 2 55 ILE cc_start: 0.8333 (mm) cc_final: 0.7295 (mm) REVERT: 2 113 THR cc_start: 0.8825 (p) cc_final: 0.8340 (t) REVERT: 2 307 LYS cc_start: 0.8428 (ptmt) cc_final: 0.7839 (ptmm) REVERT: 2 388 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7176 (mtt90) REVERT: 2 476 ARG cc_start: 0.8081 (tmt170) cc_final: 0.7424 (tpt90) REVERT: 3 70 GLU cc_start: 0.7543 (pt0) cc_final: 0.7202 (pt0) REVERT: 3 118 ILE cc_start: 0.8656 (pt) cc_final: 0.8253 (pt) REVERT: 3 146 LEU cc_start: 0.8400 (tp) cc_final: 0.7798 (tp) REVERT: 3 180 MET cc_start: 0.7266 (mmm) cc_final: 0.7025 (mmm) REVERT: 3 187 GLN cc_start: 0.7569 (mt0) cc_final: 0.7326 (mt0) REVERT: 3 205 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7258 (tm-30) REVERT: 3 206 ILE cc_start: 0.8780 (mt) cc_final: 0.8514 (mt) REVERT: 3 377 ILE cc_start: 0.8176 (mm) cc_final: 0.7878 (mm) REVERT: 3 392 ILE cc_start: 0.8474 (mt) cc_final: 0.8193 (mt) REVERT: 3 439 VAL cc_start: 0.7617 (m) cc_final: 0.6674 (m) REVERT: 3 489 LYS cc_start: 0.8693 (pttm) cc_final: 0.8279 (pptt) REVERT: 3 491 MET cc_start: 0.5890 (mtt) cc_final: 0.5554 (ppp) REVERT: 4 70 GLU cc_start: 0.7763 (pt0) cc_final: 0.7208 (pt0) REVERT: 4 113 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7613 (tm-30) REVERT: 4 152 ASP cc_start: 0.7694 (t0) cc_final: 0.7221 (p0) REVERT: 4 234 MET cc_start: 0.7650 (mtp) cc_final: 0.7374 (mtp) REVERT: 4 248 PHE cc_start: 0.7524 (m-80) cc_final: 0.7247 (m-80) REVERT: 4 290 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6517 (pt0) REVERT: 4 340 ARG cc_start: 0.7599 (ptt90) cc_final: 0.7164 (ptt90) REVERT: 4 421 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8246 (mm-40) REVERT: 5 61 ASP cc_start: 0.7966 (p0) cc_final: 0.7724 (p0) REVERT: 5 119 LEU cc_start: 0.8800 (tp) cc_final: 0.8488 (tp) REVERT: 5 244 PHE cc_start: 0.8220 (m-10) cc_final: 0.7928 (m-10) REVERT: 5 435 MET cc_start: 0.6584 (mtp) cc_final: 0.6316 (mtp) REVERT: 5 485 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7067 (mmm160) REVERT: 7 23 LEU cc_start: 0.7735 (tp) cc_final: 0.7433 (tt) REVERT: 7 112 TYR cc_start: 0.5463 (t80) cc_final: 0.5033 (t80) REVERT: 7 211 ILE cc_start: 0.6201 (mt) cc_final: 0.4086 (mt) REVERT: 8 50 ARG cc_start: 0.6467 (mmp80) cc_final: 0.5659 (mmp80) REVERT: 8 54 MET cc_start: 0.7588 (mpp) cc_final: 0.7109 (mpp) REVERT: 8 72 MET cc_start: 0.8252 (mtm) cc_final: 0.7648 (tpt) REVERT: 8 185 ASN cc_start: 0.8828 (p0) cc_final: 0.8543 (p0) REVERT: 8 203 ILE cc_start: 0.9535 (mm) cc_final: 0.9331 (mm) REVERT: 9 53 ILE cc_start: 0.8101 (pt) cc_final: 0.7896 (tp) REVERT: 9 57 TYR cc_start: 0.6410 (t80) cc_final: 0.6156 (t80) REVERT: 9 154 MET cc_start: 0.8254 (mmp) cc_final: 0.7945 (mmm) REVERT: 9 197 GLU cc_start: 0.8251 (mp0) cc_final: 0.7891 (mp0) REVERT: 9 207 MET cc_start: 0.7322 (mmp) cc_final: 0.6770 (mmt) REVERT: Q 125 TYR cc_start: 0.7830 (m-10) cc_final: 0.7516 (m-80) REVERT: Q 132 MET cc_start: 0.6978 (mtt) cc_final: 0.6196 (mtp) REVERT: Q 140 ASP cc_start: 0.7967 (m-30) cc_final: 0.7220 (t0) REVERT: Q 201 ASP cc_start: 0.8747 (t0) cc_final: 0.8516 (t70) REVERT: R 45 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6053 (tm-30) REVERT: R 58 LYS cc_start: 0.6248 (mttt) cc_final: 0.6023 (mttm) REVERT: T 16 LYS cc_start: 0.8219 (mttt) cc_final: 0.7079 (tttp) REVERT: T 34 LYS cc_start: 0.8408 (tppt) cc_final: 0.7796 (mttt) REVERT: V 47 TYR cc_start: 0.5762 (m-10) cc_final: 0.5523 (m-10) REVERT: X 27 GLU cc_start: 0.7438 (pp20) cc_final: 0.7088 (pp20) REVERT: X 31 ASN cc_start: 0.6269 (m-40) cc_final: 0.6050 (m-40) REVERT: X 51 THR cc_start: 0.8298 (m) cc_final: 0.8043 (t) REVERT: 6 66 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6921 (mt-10) REVERT: 6 82 ASP cc_start: 0.5719 (t0) cc_final: 0.5256 (m-30) REVERT: 6 109 MET cc_start: 0.7592 (tmm) cc_final: 0.6391 (mtm) REVERT: 6 151 GLN cc_start: 0.6888 (mp-120) cc_final: 0.6142 (pt0) REVERT: 6 298 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6395 (mtmt) REVERT: 6 338 LEU cc_start: 0.6607 (mt) cc_final: 0.6082 (mt) REVERT: 6 341 HIS cc_start: 0.6689 (p90) cc_final: 0.5637 (m90) REVERT: U 65 MET cc_start: 0.6771 (ppp) cc_final: 0.6395 (ppp) REVERT: U 96 MET cc_start: 0.1518 (ptm) cc_final: 0.0557 (mmt) REVERT: U 147 LYS cc_start: 0.6120 (mmmm) cc_final: 0.5660 (tptt) REVERT: U 156 MET cc_start: 0.6693 (ptm) cc_final: 0.6330 (ptt) REVERT: U 165 PHE cc_start: 0.7467 (m-80) cc_final: 0.7082 (m-80) REVERT: U 234 LYS cc_start: 0.6190 (tttt) cc_final: 0.5618 (mptt) REVERT: U 256 MET cc_start: 0.6017 (mmm) cc_final: 0.5723 (mmm) REVERT: U 290 ARG cc_start: 0.5956 (tmm-80) cc_final: 0.5694 (tmm-80) REVERT: U 383 LEU cc_start: 0.6472 (mt) cc_final: 0.5271 (mt) REVERT: U 434 LYS cc_start: 0.5816 (pttm) cc_final: 0.5230 (tptt) REVERT: U 440 HIS cc_start: 0.6160 (m-70) cc_final: 0.5605 (m90) REVERT: d 38 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5372 (mt0) REVERT: d 85 MET cc_start: 0.7827 (tmm) cc_final: 0.7421 (tmm) REVERT: d 128 LYS cc_start: 0.8601 (mmpt) cc_final: 0.8325 (mptt) REVERT: d 189 TYR cc_start: 0.6825 (t80) cc_final: 0.6182 (t80) REVERT: d 262 GLU cc_start: 0.6678 (tp30) cc_final: 0.5761 (mt-10) REVERT: d 278 PHE cc_start: 0.5967 (m-80) cc_final: 0.5646 (m-80) REVERT: d 294 PHE cc_start: 0.7124 (m-10) cc_final: 0.6718 (m-80) REVERT: d 346 ASN cc_start: 0.7209 (t0) cc_final: 0.6953 (t0) REVERT: d 349 PRO cc_start: 0.7613 (Cg_endo) cc_final: 0.7267 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8560 (tptm) cc_final: 0.8161 (tptp) REVERT: a 61 MET cc_start: 0.8093 (mtm) cc_final: 0.7579 (ptp) REVERT: a 66 ARG cc_start: 0.8066 (mpt180) cc_final: 0.7812 (mmt-90) REVERT: a 80 MET cc_start: 0.4329 (mmt) cc_final: 0.2707 (ptt) REVERT: a 129 LYS cc_start: 0.7422 (pttp) cc_final: 0.7202 (pttp) REVERT: a 283 GLU cc_start: 0.6917 (tm-30) cc_final: 0.6691 (tm-30) REVERT: a 290 LEU cc_start: 0.7945 (mt) cc_final: 0.7476 (tt) REVERT: a 329 GLU cc_start: 0.7405 (tt0) cc_final: 0.6384 (mp0) REVERT: a 383 ASN cc_start: 0.8771 (t0) cc_final: 0.8359 (m-40) REVERT: a 386 ASP cc_start: 0.7929 (m-30) cc_final: 0.7679 (m-30) REVERT: a 470 ILE cc_start: 0.6976 (mt) cc_final: 0.6772 (mt) REVERT: a 486 TRP cc_start: 0.4799 (m100) cc_final: 0.4118 (m100) REVERT: a 565 PHE cc_start: 0.7270 (m-80) cc_final: 0.6898 (m-80) REVERT: a 635 MET cc_start: 0.4422 (mmt) cc_final: 0.3912 (tpt) REVERT: a 740 TYR cc_start: 0.8443 (m-80) cc_final: 0.7592 (m-80) REVERT: a 769 ARG cc_start: 0.5638 (mtm180) cc_final: 0.4894 (mmt180) REVERT: a 831 HIS cc_start: 0.6694 (p90) cc_final: 0.6223 (p-80) REVERT: e 40 MET cc_start: 0.6399 (tmm) cc_final: 0.5933 (tmm) REVERT: e 52 TRP cc_start: 0.7151 (t-100) cc_final: 0.6927 (t-100) REVERT: e 57 LEU cc_start: 0.7904 (mt) cc_final: 0.7579 (mt) REVERT: c 363 PHE cc_start: 0.6278 (t80) cc_final: 0.5537 (t80) REVERT: c 376 ASN cc_start: 0.7635 (m110) cc_final: 0.7321 (m110) REVERT: c 394 GLN cc_start: 0.7908 (mm110) cc_final: 0.7477 (mm110) REVERT: c 429 MET cc_start: 0.7849 (mmm) cc_final: 0.7588 (mmm) outliers start: 5 outliers final: 0 residues processed: 1992 average time/residue: 0.5865 time to fit residues: 2012.1848 Evaluate side-chains 1679 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1679 time to evaluate : 5.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 668 optimal weight: 3.9990 chunk 455 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 598 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 685 optimal weight: 0.9980 chunk 555 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 410 optimal weight: 1.9990 chunk 720 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN 3 251 ASN 4 156 GLN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 461 ASN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 206 GLN 9 126 GLN ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN ** X 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 17 ASN U 91 GLN U 259 HIS U 442 HIS a 114 ASN a 285 HIS a 350 HIS ** a 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 66820 Z= 0.187 Angle : 0.571 11.008 90305 Z= 0.298 Chirality : 0.041 0.281 10236 Planarity : 0.004 0.138 11580 Dihedral : 4.341 78.393 9108 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 0.01 % Allowed : 1.91 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 8319 helix: 1.78 (0.08), residues: 4662 sheet: 0.23 (0.21), residues: 681 loop : -1.29 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP e 17 HIS 0.013 0.001 HIS a 350 PHE 0.044 0.002 PHE 6 287 TYR 0.031 0.001 TYR 3 423 ARG 0.007 0.000 ARG h 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1985 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1984 time to evaluate : 6.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8998 (pt) cc_final: 0.8718 (tp) REVERT: b 50 SER cc_start: 0.8222 (t) cc_final: 0.7925 (p) REVERT: b 89 LYS cc_start: 0.7279 (tttt) cc_final: 0.6795 (tppt) REVERT: b 146 LEU cc_start: 0.8690 (mm) cc_final: 0.8038 (mt) REVERT: b 168 GLN cc_start: 0.6906 (pp30) cc_final: 0.6700 (pp30) REVERT: b 173 PHE cc_start: 0.7139 (t80) cc_final: 0.6629 (t80) REVERT: g 28 MET cc_start: 0.8984 (mtp) cc_final: 0.8766 (mtp) REVERT: g 61 MET cc_start: 0.8150 (mmm) cc_final: 0.7869 (mmm) REVERT: h 28 MET cc_start: 0.6784 (mmm) cc_final: 0.6481 (mmp) REVERT: h 57 ILE cc_start: 0.7324 (mm) cc_final: 0.6795 (mm) REVERT: h 61 MET cc_start: 0.8383 (mtp) cc_final: 0.7841 (mmm) REVERT: h 144 TYR cc_start: 0.8451 (m-10) cc_final: 0.8197 (m-10) REVERT: i 68 TYR cc_start: 0.8066 (m-80) cc_final: 0.7719 (m-80) REVERT: i 82 ASP cc_start: 0.7162 (m-30) cc_final: 0.6280 (t0) REVERT: i 84 ILE cc_start: 0.5212 (tt) cc_final: 0.4836 (pt) REVERT: i 155 LYS cc_start: 0.5678 (mmtt) cc_final: 0.5303 (mmmt) REVERT: j 28 MET cc_start: 0.8823 (mtp) cc_final: 0.8494 (mtp) REVERT: j 51 LEU cc_start: 0.8236 (pp) cc_final: 0.7219 (tt) REVERT: k 28 MET cc_start: 0.6075 (ttt) cc_final: 0.5745 (mtp) REVERT: l 14 PHE cc_start: 0.7790 (m-80) cc_final: 0.7379 (m-80) REVERT: l 23 MET cc_start: 0.6984 (ptt) cc_final: 0.6729 (ptt) REVERT: l 44 MET cc_start: 0.6593 (tpp) cc_final: 0.5596 (mmt) REVERT: l 51 LEU cc_start: 0.6408 (mp) cc_final: 0.6113 (mp) REVERT: l 53 MET cc_start: 0.8055 (mmm) cc_final: 0.6498 (tmm) REVERT: l 61 MET cc_start: 0.1482 (mtp) cc_final: 0.1069 (mtp) REVERT: l 131 MET cc_start: 0.7275 (ttp) cc_final: 0.6836 (ttp) REVERT: n 24 VAL cc_start: 0.6327 (m) cc_final: 0.6061 (m) REVERT: n 61 MET cc_start: 0.6716 (mmm) cc_final: 0.6278 (mmm) REVERT: n 70 LEU cc_start: 0.7529 (mt) cc_final: 0.7292 (mt) REVERT: n 127 LEU cc_start: 0.6934 (mm) cc_final: 0.6352 (pt) REVERT: o 32 TYR cc_start: 0.8337 (t80) cc_final: 0.8020 (t80) REVERT: o 70 LEU cc_start: 0.8803 (mt) cc_final: 0.8509 (mt) REVERT: o 144 TYR cc_start: 0.7848 (m-80) cc_final: 0.7428 (m-80) REVERT: 1 232 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6215 (mtm-85) REVERT: 1 242 GLN cc_start: 0.7680 (tt0) cc_final: 0.7330 (tt0) REVERT: 1 279 GLU cc_start: 0.7242 (pm20) cc_final: 0.5406 (mm-30) REVERT: 1 306 MET cc_start: 0.7843 (mmm) cc_final: 0.7581 (tpt) REVERT: 1 311 LEU cc_start: 0.9169 (mt) cc_final: 0.8918 (mt) REVERT: 1 328 TYR cc_start: 0.7807 (m-10) cc_final: 0.7294 (m-80) REVERT: 1 508 THR cc_start: 0.6333 (m) cc_final: 0.5954 (p) REVERT: 1 522 GLN cc_start: 0.7812 (tt0) cc_final: 0.7556 (tt0) REVERT: 0 53 GLU cc_start: 0.8080 (tp30) cc_final: 0.7737 (tp30) REVERT: 0 214 VAL cc_start: 0.8245 (t) cc_final: 0.7962 (t) REVERT: 0 314 ASN cc_start: 0.8475 (t0) cc_final: 0.8242 (t0) REVERT: 0 356 GLU cc_start: 0.7927 (mt-10) cc_final: 0.6924 (tm-30) REVERT: 0 394 CYS cc_start: 0.8706 (m) cc_final: 0.8450 (t) REVERT: 0 445 PHE cc_start: 0.6830 (p90) cc_final: 0.5553 (m-10) REVERT: 0 456 LYS cc_start: 0.8512 (mmpt) cc_final: 0.7890 (mtmt) REVERT: 0 531 PHE cc_start: 0.5776 (t80) cc_final: 0.4950 (t80) REVERT: 2 34 MET cc_start: 0.7335 (tmm) cc_final: 0.6900 (tmm) REVERT: 2 55 ILE cc_start: 0.8338 (mm) cc_final: 0.7344 (mm) REVERT: 2 113 THR cc_start: 0.8820 (p) cc_final: 0.8327 (t) REVERT: 2 318 MET cc_start: 0.8355 (mmm) cc_final: 0.7987 (mtp) REVERT: 2 476 ARG cc_start: 0.8059 (tmt170) cc_final: 0.7388 (tpt90) REVERT: 2 486 GLU cc_start: 0.4931 (tm-30) cc_final: 0.4676 (tm-30) REVERT: 2 608 MET cc_start: 0.6478 (mmp) cc_final: 0.6195 (mmp) REVERT: 3 70 GLU cc_start: 0.7317 (pt0) cc_final: 0.7053 (pt0) REVERT: 3 118 ILE cc_start: 0.8754 (pt) cc_final: 0.8433 (pt) REVERT: 3 146 LEU cc_start: 0.8332 (tp) cc_final: 0.7700 (tp) REVERT: 3 180 MET cc_start: 0.7389 (mmm) cc_final: 0.7041 (mmm) REVERT: 3 205 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7185 (tm-30) REVERT: 3 206 ILE cc_start: 0.8718 (mt) cc_final: 0.8501 (mt) REVERT: 3 227 PHE cc_start: 0.6824 (m-80) cc_final: 0.6360 (m-10) REVERT: 3 374 GLU cc_start: 0.8767 (pm20) cc_final: 0.7968 (pm20) REVERT: 3 377 ILE cc_start: 0.8202 (mm) cc_final: 0.7943 (mm) REVERT: 3 392 ILE cc_start: 0.8428 (mt) cc_final: 0.8198 (mt) REVERT: 3 489 LYS cc_start: 0.8569 (pttm) cc_final: 0.8239 (pptt) REVERT: 3 491 MET cc_start: 0.6722 (mtt) cc_final: 0.5871 (ppp) REVERT: 4 70 GLU cc_start: 0.7770 (pt0) cc_final: 0.7173 (pt0) REVERT: 4 113 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7751 (tm-30) REVERT: 4 152 ASP cc_start: 0.7709 (t0) cc_final: 0.7148 (p0) REVERT: 4 290 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6339 (pt0) REVERT: 4 336 GLU cc_start: 0.7971 (tt0) cc_final: 0.7686 (tt0) REVERT: 4 340 ARG cc_start: 0.7611 (ptt90) cc_final: 0.7158 (ptt90) REVERT: 4 356 MET cc_start: 0.7998 (mtm) cc_final: 0.7738 (mtm) REVERT: 5 61 ASP cc_start: 0.8090 (p0) cc_final: 0.7806 (p0) REVERT: 5 119 LEU cc_start: 0.8827 (tp) cc_final: 0.8507 (tp) REVERT: 5 238 MET cc_start: 0.8125 (mmp) cc_final: 0.7806 (mmp) REVERT: 5 244 PHE cc_start: 0.8289 (m-10) cc_final: 0.7944 (m-10) REVERT: 5 248 PHE cc_start: 0.6848 (m-10) cc_final: 0.6564 (m-80) REVERT: 5 435 MET cc_start: 0.6586 (mtp) cc_final: 0.6245 (mtp) REVERT: 5 478 ASP cc_start: 0.8128 (m-30) cc_final: 0.7900 (m-30) REVERT: 5 485 ARG cc_start: 0.7511 (mtp180) cc_final: 0.7090 (mmm160) REVERT: 5 491 MET cc_start: 0.6608 (mtp) cc_final: 0.6166 (mtp) REVERT: 7 23 LEU cc_start: 0.7703 (tp) cc_final: 0.7382 (tt) REVERT: 7 56 MET cc_start: 0.7558 (tpp) cc_final: 0.7231 (tpp) REVERT: 7 112 TYR cc_start: 0.5369 (t80) cc_final: 0.5156 (t80) REVERT: 7 163 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7390 (mtpt) REVERT: 7 170 ASN cc_start: 0.6256 (m-40) cc_final: 0.5878 (t0) REVERT: 7 211 ILE cc_start: 0.6191 (mt) cc_final: 0.4127 (mt) REVERT: 8 50 ARG cc_start: 0.6301 (mmp80) cc_final: 0.5616 (mmp80) REVERT: 8 54 MET cc_start: 0.7803 (mpp) cc_final: 0.7312 (mpp) REVERT: 8 59 LYS cc_start: 0.7663 (mmmm) cc_final: 0.6907 (pptt) REVERT: 8 72 MET cc_start: 0.8379 (mtm) cc_final: 0.7700 (tpt) REVERT: 8 185 ASN cc_start: 0.8798 (p0) cc_final: 0.8496 (p0) REVERT: 8 203 ILE cc_start: 0.9515 (mm) cc_final: 0.9312 (mm) REVERT: 9 44 ARG cc_start: 0.6756 (ppt170) cc_final: 0.6509 (ptm160) REVERT: 9 154 MET cc_start: 0.8258 (mmp) cc_final: 0.7918 (mmm) REVERT: 9 197 GLU cc_start: 0.8218 (mp0) cc_final: 0.7812 (mp0) REVERT: 9 207 MET cc_start: 0.7315 (mmp) cc_final: 0.6880 (mmt) REVERT: Q 132 MET cc_start: 0.7018 (mtt) cc_final: 0.6175 (mtp) REVERT: Q 140 ASP cc_start: 0.7937 (m-30) cc_final: 0.7077 (t0) REVERT: R 21 LYS cc_start: 0.5147 (mmmm) cc_final: 0.4794 (pptt) REVERT: R 47 TYR cc_start: 0.6821 (m-80) cc_final: 0.6587 (m-80) REVERT: R 58 LYS cc_start: 0.6100 (mttt) cc_final: 0.5830 (mttm) REVERT: T 16 LYS cc_start: 0.8157 (mttt) cc_final: 0.7015 (tttp) REVERT: T 34 LYS cc_start: 0.8420 (tppt) cc_final: 0.7821 (mttt) REVERT: V 47 TYR cc_start: 0.5749 (m-10) cc_final: 0.5492 (m-10) REVERT: X 27 GLU cc_start: 0.7453 (pp20) cc_final: 0.7057 (pp20) REVERT: X 31 ASN cc_start: 0.6248 (m-40) cc_final: 0.6035 (m-40) REVERT: X 51 THR cc_start: 0.8306 (m) cc_final: 0.8032 (t) REVERT: 6 66 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6972 (mt-10) REVERT: 6 82 ASP cc_start: 0.5534 (t0) cc_final: 0.4945 (m-30) REVERT: 6 109 MET cc_start: 0.7579 (tmm) cc_final: 0.6620 (ttm) REVERT: 6 298 LYS cc_start: 0.6582 (mmtt) cc_final: 0.6341 (mtmt) REVERT: 6 301 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6622 (tpp80) REVERT: 6 338 LEU cc_start: 0.6708 (mt) cc_final: 0.6193 (mt) REVERT: 6 341 HIS cc_start: 0.6719 (p90) cc_final: 0.5662 (m90) REVERT: U 96 MET cc_start: 0.1363 (ptm) cc_final: 0.0525 (mmt) REVERT: U 147 LYS cc_start: 0.6126 (mmmm) cc_final: 0.5645 (tptt) REVERT: U 156 MET cc_start: 0.6636 (ptm) cc_final: 0.6320 (ptt) REVERT: U 165 PHE cc_start: 0.7391 (m-80) cc_final: 0.6969 (m-80) REVERT: U 234 LYS cc_start: 0.6209 (tttt) cc_final: 0.5631 (mptt) REVERT: U 256 MET cc_start: 0.6108 (mmm) cc_final: 0.5785 (mmm) REVERT: U 321 LEU cc_start: 0.7978 (mm) cc_final: 0.7723 (mm) REVERT: U 324 GLN cc_start: 0.7431 (mp10) cc_final: 0.7147 (mp10) REVERT: U 383 LEU cc_start: 0.6487 (mt) cc_final: 0.5480 (mt) REVERT: U 434 LYS cc_start: 0.5795 (pttm) cc_final: 0.5274 (tptt) REVERT: U 440 HIS cc_start: 0.6327 (m-70) cc_final: 0.5766 (m-70) REVERT: U 460 MET cc_start: 0.6670 (tpp) cc_final: 0.5793 (tpp) REVERT: d 38 GLN cc_start: 0.6266 (mm-40) cc_final: 0.5470 (mt0) REVERT: d 75 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8055 (mmmt) REVERT: d 85 MET cc_start: 0.7893 (tmm) cc_final: 0.7541 (tmm) REVERT: d 165 GLN cc_start: 0.7250 (tt0) cc_final: 0.6313 (tp-100) REVERT: d 189 TYR cc_start: 0.6980 (t80) cc_final: 0.6271 (t80) REVERT: d 262 GLU cc_start: 0.6680 (tp30) cc_final: 0.5808 (mt-10) REVERT: d 294 PHE cc_start: 0.7133 (m-10) cc_final: 0.6798 (m-80) REVERT: d 349 PRO cc_start: 0.7622 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8500 (tptm) cc_final: 0.8090 (tptp) REVERT: a 61 MET cc_start: 0.7935 (mtm) cc_final: 0.7571 (ptp) REVERT: a 66 ARG cc_start: 0.8073 (mpt180) cc_final: 0.7812 (mmt-90) REVERT: a 80 MET cc_start: 0.4518 (mmt) cc_final: 0.2847 (ptt) REVERT: a 124 GLU cc_start: 0.6493 (tp30) cc_final: 0.5262 (pp20) REVERT: a 125 LEU cc_start: 0.6439 (mt) cc_final: 0.5998 (mt) REVERT: a 129 LYS cc_start: 0.7402 (pttp) cc_final: 0.7189 (pttp) REVERT: a 290 LEU cc_start: 0.7889 (mt) cc_final: 0.7392 (tt) REVERT: a 329 GLU cc_start: 0.7490 (tt0) cc_final: 0.6376 (mp0) REVERT: a 383 ASN cc_start: 0.8782 (t0) cc_final: 0.8464 (m-40) REVERT: a 470 ILE cc_start: 0.7015 (mt) cc_final: 0.6781 (mt) REVERT: a 565 PHE cc_start: 0.7306 (m-80) cc_final: 0.7001 (m-80) REVERT: a 610 SER cc_start: 0.8112 (t) cc_final: 0.7733 (m) REVERT: a 623 MET cc_start: 0.8509 (ttp) cc_final: 0.8201 (tpp) REVERT: a 635 MET cc_start: 0.4402 (mmt) cc_final: 0.3938 (tpt) REVERT: a 740 TYR cc_start: 0.8375 (m-80) cc_final: 0.7670 (m-80) REVERT: a 769 ARG cc_start: 0.5596 (mtm180) cc_final: 0.4835 (mmt180) REVERT: e 16 PHE cc_start: 0.5676 (t80) cc_final: 0.5410 (t80) REVERT: f 29 LEU cc_start: 0.8342 (tp) cc_final: 0.8107 (tp) REVERT: c 317 PHE cc_start: 0.1804 (m-80) cc_final: 0.1472 (m-80) REVERT: c 363 PHE cc_start: 0.6126 (t80) cc_final: 0.5342 (t80) REVERT: c 376 ASN cc_start: 0.7532 (m110) cc_final: 0.7180 (m110) REVERT: c 394 GLN cc_start: 0.7871 (mm110) cc_final: 0.7465 (mm110) REVERT: c 429 MET cc_start: 0.7829 (mmm) cc_final: 0.7553 (mmm) outliers start: 1 outliers final: 0 residues processed: 1985 average time/residue: 0.5778 time to fit residues: 1978.2738 Evaluate side-chains 1676 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1676 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 270 optimal weight: 3.9990 chunk 723 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 471 optimal weight: 1.9990 chunk 198 optimal weight: 0.7980 chunk 804 optimal weight: 6.9990 chunk 667 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 422 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 484 GLN ** 0 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 573 HIS 2 207 GLN ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 156 GLN 5 482 GLN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 23 HIS 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 17 ASN ** U 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 HIS d 84 HIS a 285 HIS ** a 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 496 ASN a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 66820 Z= 0.207 Angle : 0.591 10.906 90305 Z= 0.308 Chirality : 0.041 0.230 10236 Planarity : 0.004 0.145 11580 Dihedral : 4.380 77.413 9108 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 0.08 % Allowed : 1.86 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.09), residues: 8319 helix: 1.70 (0.08), residues: 4695 sheet: 0.12 (0.20), residues: 699 loop : -1.35 (0.12), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP U 376 HIS 0.008 0.001 HIS U 259 PHE 0.069 0.002 PHE c 433 TYR 0.041 0.002 TYR g 68 ARG 0.007 0.000 ARG j 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1941 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1935 time to evaluate : 5.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8955 (pt) cc_final: 0.8678 (tp) REVERT: b 34 ARG cc_start: 0.6137 (tpp80) cc_final: 0.5791 (ttm-80) REVERT: b 43 GLU cc_start: 0.6807 (tp30) cc_final: 0.6486 (tp30) REVERT: b 89 LYS cc_start: 0.7409 (tttt) cc_final: 0.6891 (tppt) REVERT: b 146 LEU cc_start: 0.8417 (mm) cc_final: 0.8008 (tp) REVERT: b 168 GLN cc_start: 0.6885 (pp30) cc_final: 0.6676 (pp30) REVERT: b 173 PHE cc_start: 0.7252 (t80) cc_final: 0.6782 (t80) REVERT: h 28 MET cc_start: 0.6775 (mmm) cc_final: 0.6305 (mmp) REVERT: h 51 LEU cc_start: 0.7140 (mt) cc_final: 0.6713 (mt) REVERT: h 57 ILE cc_start: 0.7230 (mm) cc_final: 0.6707 (mm) REVERT: h 61 MET cc_start: 0.8397 (mtp) cc_final: 0.7838 (mmm) REVERT: h 119 ARG cc_start: 0.6237 (mmp80) cc_final: 0.5862 (mmp80) REVERT: h 144 TYR cc_start: 0.8485 (m-10) cc_final: 0.8216 (m-10) REVERT: i 23 MET cc_start: 0.6276 (ttm) cc_final: 0.5510 (ttm) REVERT: i 68 TYR cc_start: 0.8232 (m-80) cc_final: 0.7643 (m-80) REVERT: i 84 ILE cc_start: 0.5362 (tt) cc_final: 0.4961 (pt) REVERT: i 155 LYS cc_start: 0.5621 (mmtt) cc_final: 0.5231 (mmmt) REVERT: j 28 MET cc_start: 0.8690 (mtp) cc_final: 0.8405 (mtp) REVERT: j 51 LEU cc_start: 0.8219 (pp) cc_final: 0.7192 (tt) REVERT: j 84 ILE cc_start: 0.6349 (mm) cc_final: 0.6119 (mm) REVERT: k 28 MET cc_start: 0.6103 (ttt) cc_final: 0.5776 (mtp) REVERT: l 14 PHE cc_start: 0.7846 (m-80) cc_final: 0.7404 (m-80) REVERT: l 23 MET cc_start: 0.7022 (ptt) cc_final: 0.6821 (ptt) REVERT: l 44 MET cc_start: 0.6750 (tpp) cc_final: 0.5765 (mmt) REVERT: l 51 LEU cc_start: 0.6301 (mp) cc_final: 0.6038 (mp) REVERT: l 53 MET cc_start: 0.7951 (mmm) cc_final: 0.6285 (tmm) REVERT: l 61 MET cc_start: 0.1787 (mtp) cc_final: 0.1430 (mtp) REVERT: l 131 MET cc_start: 0.7252 (ttp) cc_final: 0.6826 (ttp) REVERT: m 90 PHE cc_start: 0.4270 (m-10) cc_final: 0.3992 (m-10) REVERT: n 61 MET cc_start: 0.6818 (mmm) cc_final: 0.6432 (mmm) REVERT: n 70 LEU cc_start: 0.7442 (mt) cc_final: 0.7200 (mt) REVERT: n 82 ASP cc_start: 0.7261 (m-30) cc_final: 0.4656 (m-30) REVERT: n 86 LEU cc_start: 0.7250 (tp) cc_final: 0.6358 (tp) REVERT: o 32 TYR cc_start: 0.8357 (t80) cc_final: 0.8010 (t80) REVERT: o 55 SER cc_start: 0.7900 (p) cc_final: 0.7687 (p) REVERT: o 70 LEU cc_start: 0.8795 (mt) cc_final: 0.8479 (mt) REVERT: o 144 TYR cc_start: 0.8071 (m-10) cc_final: 0.7607 (m-80) REVERT: 1 86 LEU cc_start: 0.8146 (tp) cc_final: 0.7446 (tp) REVERT: 1 219 GLU cc_start: 0.9100 (pm20) cc_final: 0.8722 (pm20) REVERT: 1 232 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6084 (mtm-85) REVERT: 1 242 GLN cc_start: 0.7778 (tt0) cc_final: 0.7409 (tt0) REVERT: 1 261 GLN cc_start: 0.8384 (mp10) cc_final: 0.8128 (mp10) REVERT: 1 279 GLU cc_start: 0.7128 (pm20) cc_final: 0.5459 (mm-30) REVERT: 1 306 MET cc_start: 0.7946 (mmm) cc_final: 0.7710 (tpt) REVERT: 1 328 TYR cc_start: 0.7895 (m-10) cc_final: 0.7251 (m-80) REVERT: 1 522 GLN cc_start: 0.7821 (tt0) cc_final: 0.7539 (tt0) REVERT: 1 541 LEU cc_start: 0.8767 (tt) cc_final: 0.8452 (tt) REVERT: 0 53 GLU cc_start: 0.8068 (tp30) cc_final: 0.7518 (mm-30) REVERT: 0 158 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7532 (mm-30) REVERT: 0 314 ASN cc_start: 0.8722 (t0) cc_final: 0.8468 (t0) REVERT: 0 353 ARG cc_start: 0.7391 (mpp80) cc_final: 0.6788 (mpp80) REVERT: 0 356 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7073 (tm-30) REVERT: 0 374 TYR cc_start: 0.8365 (m-80) cc_final: 0.8130 (m-10) REVERT: 0 394 CYS cc_start: 0.8754 (m) cc_final: 0.8551 (m) REVERT: 0 419 ASP cc_start: 0.7072 (t0) cc_final: 0.6848 (t0) REVERT: 0 445 PHE cc_start: 0.6595 (p90) cc_final: 0.5332 (m-10) REVERT: 0 456 LYS cc_start: 0.8568 (mmpt) cc_final: 0.7896 (mtmt) REVERT: 0 478 LYS cc_start: 0.7015 (mtmt) cc_final: 0.6363 (mmtp) REVERT: 0 531 PHE cc_start: 0.5779 (t80) cc_final: 0.4843 (t80) REVERT: 2 34 MET cc_start: 0.7433 (tmm) cc_final: 0.6981 (tmm) REVERT: 2 113 THR cc_start: 0.8817 (p) cc_final: 0.8346 (t) REVERT: 2 207 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5967 (pm20) REVERT: 2 307 LYS cc_start: 0.8513 (ptmt) cc_final: 0.7940 (ptmm) REVERT: 2 476 ARG cc_start: 0.8067 (tmt170) cc_final: 0.7546 (tpt90) REVERT: 2 486 GLU cc_start: 0.4893 (tm-30) cc_final: 0.4654 (tm-30) REVERT: 2 608 MET cc_start: 0.6261 (mmp) cc_final: 0.5895 (mmp) REVERT: 3 70 GLU cc_start: 0.7355 (pt0) cc_final: 0.7123 (pt0) REVERT: 3 105 ILE cc_start: 0.8610 (mt) cc_final: 0.8405 (mt) REVERT: 3 146 LEU cc_start: 0.8262 (tp) cc_final: 0.7768 (tp) REVERT: 3 180 MET cc_start: 0.7661 (mmm) cc_final: 0.7394 (mmm) REVERT: 3 202 ILE cc_start: 0.8857 (mt) cc_final: 0.8626 (mt) REVERT: 3 206 ILE cc_start: 0.8794 (mt) cc_final: 0.8575 (mt) REVERT: 3 227 PHE cc_start: 0.6925 (m-80) cc_final: 0.6524 (m-10) REVERT: 3 266 ASP cc_start: 0.9074 (m-30) cc_final: 0.8729 (m-30) REVERT: 3 392 ILE cc_start: 0.8527 (mt) cc_final: 0.8271 (mt) REVERT: 3 489 LYS cc_start: 0.8639 (pttm) cc_final: 0.8263 (pptt) REVERT: 3 491 MET cc_start: 0.6582 (mtt) cc_final: 0.5606 (ppp) REVERT: 4 70 GLU cc_start: 0.7827 (pt0) cc_final: 0.7181 (pt0) REVERT: 4 113 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7520 (tm-30) REVERT: 4 148 GLU cc_start: 0.8360 (tt0) cc_final: 0.7913 (tm-30) REVERT: 4 152 ASP cc_start: 0.7738 (t0) cc_final: 0.7128 (p0) REVERT: 4 290 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6233 (pt0) REVERT: 4 340 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7203 (ptt90) REVERT: 4 356 MET cc_start: 0.8067 (mtm) cc_final: 0.7738 (mtm) REVERT: 4 421 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7718 (mm-40) REVERT: 5 61 ASP cc_start: 0.7864 (p0) cc_final: 0.7575 (p0) REVERT: 5 119 LEU cc_start: 0.8833 (tp) cc_final: 0.8519 (tp) REVERT: 5 202 ILE cc_start: 0.9124 (mt) cc_final: 0.8732 (mt) REVERT: 5 208 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7161 (ptp90) REVERT: 5 238 MET cc_start: 0.8057 (mmp) cc_final: 0.7711 (mmp) REVERT: 5 244 PHE cc_start: 0.8321 (m-10) cc_final: 0.8052 (m-10) REVERT: 7 23 LEU cc_start: 0.7674 (tp) cc_final: 0.7369 (tt) REVERT: 7 56 MET cc_start: 0.7557 (tpp) cc_final: 0.7298 (tpp) REVERT: 7 112 TYR cc_start: 0.5376 (t80) cc_final: 0.5025 (t80) REVERT: 7 211 ILE cc_start: 0.6289 (mt) cc_final: 0.4236 (mt) REVERT: 8 50 ARG cc_start: 0.6296 (mmp80) cc_final: 0.5733 (mmp80) REVERT: 8 54 MET cc_start: 0.7934 (mpp) cc_final: 0.7252 (mpp) REVERT: 8 72 MET cc_start: 0.8403 (mtm) cc_final: 0.7714 (tpt) REVERT: 8 185 ASN cc_start: 0.8830 (p0) cc_final: 0.8544 (p0) REVERT: 9 154 MET cc_start: 0.8300 (mmp) cc_final: 0.7787 (mmt) REVERT: 9 197 GLU cc_start: 0.8239 (mp0) cc_final: 0.7940 (mp0) REVERT: 9 207 MET cc_start: 0.7165 (mmp) cc_final: 0.6834 (mmt) REVERT: Q 85 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6699 (mmm160) REVERT: Q 125 TYR cc_start: 0.8026 (m-10) cc_final: 0.7768 (m-80) REVERT: Q 132 MET cc_start: 0.7099 (mtt) cc_final: 0.6188 (mtp) REVERT: R 47 TYR cc_start: 0.6895 (m-80) cc_final: 0.6638 (m-80) REVERT: R 58 LYS cc_start: 0.5957 (mttt) cc_final: 0.5612 (mttm) REVERT: T 16 LYS cc_start: 0.8178 (mttt) cc_final: 0.7098 (tttp) REVERT: V 47 TYR cc_start: 0.5903 (m-10) cc_final: 0.5403 (m-10) REVERT: X 27 GLU cc_start: 0.7316 (pp20) cc_final: 0.7021 (pp20) REVERT: X 51 THR cc_start: 0.8270 (m) cc_final: 0.8034 (t) REVERT: 6 66 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6821 (mt-10) REVERT: 6 82 ASP cc_start: 0.5276 (t0) cc_final: 0.4915 (m-30) REVERT: 6 109 MET cc_start: 0.7589 (tmm) cc_final: 0.6600 (ttm) REVERT: 6 151 GLN cc_start: 0.6945 (mp-120) cc_final: 0.5987 (pt0) REVERT: 6 301 ARG cc_start: 0.6788 (ttm170) cc_final: 0.6320 (ttm170) REVERT: 6 338 LEU cc_start: 0.6741 (mt) cc_final: 0.6230 (mt) REVERT: 6 341 HIS cc_start: 0.6676 (p90) cc_final: 0.5538 (m90) REVERT: U 65 MET cc_start: 0.6631 (ppp) cc_final: 0.5368 (mtt) REVERT: U 96 MET cc_start: 0.1372 (ptm) cc_final: 0.0524 (mmt) REVERT: U 147 LYS cc_start: 0.6250 (mmmm) cc_final: 0.5755 (tptt) REVERT: U 156 MET cc_start: 0.6662 (ptm) cc_final: 0.6336 (ptt) REVERT: U 216 PHE cc_start: 0.6893 (m-80) cc_final: 0.6684 (m-10) REVERT: U 234 LYS cc_start: 0.6202 (tttt) cc_final: 0.5505 (mptt) REVERT: U 321 LEU cc_start: 0.7976 (mm) cc_final: 0.7694 (mt) REVERT: U 324 GLN cc_start: 0.7466 (mp10) cc_final: 0.7027 (mp10) REVERT: U 383 LEU cc_start: 0.6610 (mt) cc_final: 0.5547 (mt) REVERT: U 418 VAL cc_start: 0.8076 (m) cc_final: 0.7591 (p) REVERT: U 434 LYS cc_start: 0.5731 (pttm) cc_final: 0.5248 (tptt) REVERT: d 38 GLN cc_start: 0.6494 (mm-40) cc_final: 0.5700 (mt0) REVERT: d 75 LYS cc_start: 0.8476 (mmtt) cc_final: 0.8006 (mmmt) REVERT: d 128 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8423 (mptt) REVERT: d 165 GLN cc_start: 0.7335 (tt0) cc_final: 0.6173 (tp-100) REVERT: d 175 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7093 (tt0) REVERT: d 186 TYR cc_start: 0.6397 (t80) cc_final: 0.6054 (t80) REVERT: d 189 TYR cc_start: 0.7128 (t80) cc_final: 0.6361 (t80) REVERT: d 262 GLU cc_start: 0.6898 (tp30) cc_final: 0.5998 (mt-10) REVERT: d 346 ASN cc_start: 0.6939 (t0) cc_final: 0.6607 (t0) REVERT: d 349 PRO cc_start: 0.7690 (Cg_endo) cc_final: 0.7362 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8457 (tptm) cc_final: 0.8010 (tptp) REVERT: a 66 ARG cc_start: 0.8237 (mpt180) cc_final: 0.8012 (mmt90) REVERT: a 124 GLU cc_start: 0.6418 (tp30) cc_final: 0.5233 (pp20) REVERT: a 125 LEU cc_start: 0.6364 (mt) cc_final: 0.5920 (mt) REVERT: a 129 LYS cc_start: 0.7442 (pttp) cc_final: 0.7205 (pttp) REVERT: a 290 LEU cc_start: 0.7880 (mt) cc_final: 0.7341 (tt) REVERT: a 383 ASN cc_start: 0.8810 (t0) cc_final: 0.8511 (m-40) REVERT: a 470 ILE cc_start: 0.6981 (mt) cc_final: 0.6699 (mt) REVERT: a 565 PHE cc_start: 0.7391 (m-80) cc_final: 0.6997 (m-80) REVERT: a 610 SER cc_start: 0.8085 (t) cc_final: 0.7719 (m) REVERT: a 623 MET cc_start: 0.8438 (ttp) cc_final: 0.8142 (tpp) REVERT: a 635 MET cc_start: 0.4427 (mmt) cc_final: 0.3887 (tpt) REVERT: a 740 TYR cc_start: 0.8310 (m-80) cc_final: 0.7559 (m-80) REVERT: a 769 ARG cc_start: 0.5581 (mtm180) cc_final: 0.4807 (mmt180) REVERT: e 16 PHE cc_start: 0.5598 (t80) cc_final: 0.5329 (t80) REVERT: e 57 LEU cc_start: 0.8010 (mt) cc_final: 0.7689 (mt) REVERT: f 29 LEU cc_start: 0.8356 (tp) cc_final: 0.8118 (tp) REVERT: c 317 PHE cc_start: 0.1827 (m-80) cc_final: 0.1493 (m-80) REVERT: c 376 ASN cc_start: 0.7572 (m110) cc_final: 0.7243 (m110) REVERT: c 394 GLN cc_start: 0.7908 (mm110) cc_final: 0.7501 (mm110) REVERT: c 425 THR cc_start: 0.9393 (m) cc_final: 0.9175 (m) outliers start: 6 outliers final: 3 residues processed: 1939 average time/residue: 0.5933 time to fit residues: 1967.9381 Evaluate side-chains 1669 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1665 time to evaluate : 5.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 775 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 458 optimal weight: 0.9990 chunk 587 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 676 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 chunk 800 optimal weight: 3.9990 chunk 501 optimal weight: 1.9990 chunk 488 optimal weight: 6.9990 chunk 369 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN l 7 ASN m 92 GLN o 123 GLN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 522 GLN ** 0 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 164 HIS ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN 3 251 ASN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN 8 206 GLN 9 24 ASN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 113 ASN 6 16 GLN 6 23 HIS 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 296 HIS U 17 ASN ** U 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 HIS U 442 HIS ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN a 76 ASN a 269 ASN a 419 HIS ** a 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 669 GLN ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 66820 Z= 0.227 Angle : 0.614 11.474 90305 Z= 0.320 Chirality : 0.042 0.290 10236 Planarity : 0.004 0.145 11580 Dihedral : 4.470 76.874 9108 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8319 helix: 1.62 (0.08), residues: 4700 sheet: 0.09 (0.21), residues: 692 loop : -1.40 (0.11), residues: 2927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP U 376 HIS 0.007 0.001 HIS U 259 PHE 0.037 0.002 PHE 1 612 TYR 0.038 0.002 TYR g 68 ARG 0.014 0.001 ARG 4 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1906 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1904 time to evaluate : 5.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8959 (pt) cc_final: 0.8690 (tp) REVERT: b 146 LEU cc_start: 0.8669 (mm) cc_final: 0.8150 (mp) REVERT: b 157 ILE cc_start: 0.9035 (tt) cc_final: 0.8671 (tt) REVERT: b 168 GLN cc_start: 0.6848 (pp30) cc_final: 0.6632 (pp30) REVERT: b 173 PHE cc_start: 0.7394 (t80) cc_final: 0.7093 (t80) REVERT: g 61 MET cc_start: 0.8279 (mmm) cc_final: 0.7763 (ttp) REVERT: h 28 MET cc_start: 0.6792 (mmm) cc_final: 0.6333 (mmp) REVERT: h 51 LEU cc_start: 0.7204 (mt) cc_final: 0.6710 (mt) REVERT: h 57 ILE cc_start: 0.7242 (mm) cc_final: 0.6833 (mm) REVERT: h 61 MET cc_start: 0.8457 (mtp) cc_final: 0.7871 (mmm) REVERT: h 144 TYR cc_start: 0.8525 (m-10) cc_final: 0.8235 (m-10) REVERT: i 23 MET cc_start: 0.6485 (ttm) cc_final: 0.6002 (ttm) REVERT: i 68 TYR cc_start: 0.8151 (m-80) cc_final: 0.7634 (m-80) REVERT: i 84 ILE cc_start: 0.5288 (tt) cc_final: 0.4925 (pt) REVERT: i 155 LYS cc_start: 0.5705 (mmtt) cc_final: 0.5291 (mmmt) REVERT: j 28 MET cc_start: 0.8740 (mtp) cc_final: 0.8481 (mtp) REVERT: j 51 LEU cc_start: 0.8157 (pp) cc_final: 0.7168 (tt) REVERT: j 84 ILE cc_start: 0.6400 (mm) cc_final: 0.6151 (mm) REVERT: k 24 VAL cc_start: 0.7442 (p) cc_final: 0.7167 (p) REVERT: k 28 MET cc_start: 0.6222 (ttt) cc_final: 0.5858 (mtp) REVERT: l 23 MET cc_start: 0.6975 (ptt) cc_final: 0.6732 (ptt) REVERT: l 61 MET cc_start: 0.1743 (mtp) cc_final: 0.1350 (mtp) REVERT: l 92 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6813 (mm-40) REVERT: l 121 THR cc_start: 0.5549 (m) cc_final: 0.5077 (m) REVERT: l 131 MET cc_start: 0.7197 (ttp) cc_final: 0.6839 (ttp) REVERT: m 23 MET cc_start: 0.3624 (tpt) cc_final: 0.3041 (tpt) REVERT: m 61 MET cc_start: 0.8438 (ttt) cc_final: 0.8157 (ttt) REVERT: n 28 MET cc_start: 0.6350 (mtp) cc_final: 0.6145 (tmm) REVERT: n 61 MET cc_start: 0.6807 (mmm) cc_final: 0.6467 (mmm) REVERT: n 86 LEU cc_start: 0.6833 (tp) cc_final: 0.6125 (tp) REVERT: n 127 LEU cc_start: 0.7137 (mm) cc_final: 0.6565 (pt) REVERT: o 23 MET cc_start: 0.7795 (ttt) cc_final: 0.7530 (ttt) REVERT: o 32 TYR cc_start: 0.8417 (t80) cc_final: 0.8087 (t80) REVERT: o 70 LEU cc_start: 0.8806 (mt) cc_final: 0.8113 (mt) REVERT: 1 86 LEU cc_start: 0.8210 (tp) cc_final: 0.7359 (tp) REVERT: 1 205 MET cc_start: 0.8079 (ptt) cc_final: 0.7836 (ptp) REVERT: 1 219 GLU cc_start: 0.9110 (pm20) cc_final: 0.8767 (pm20) REVERT: 1 232 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6370 (mtm-85) REVERT: 1 241 VAL cc_start: 0.7906 (t) cc_final: 0.7631 (t) REVERT: 1 279 GLU cc_start: 0.7199 (pm20) cc_final: 0.5611 (mm-30) REVERT: 1 311 LEU cc_start: 0.9075 (mt) cc_final: 0.8836 (mt) REVERT: 1 328 TYR cc_start: 0.7828 (m-10) cc_final: 0.7219 (m-80) REVERT: 1 495 LEU cc_start: 0.7964 (tp) cc_final: 0.7419 (pp) REVERT: 1 522 GLN cc_start: 0.7810 (tt0) cc_final: 0.7604 (tt0) REVERT: 1 541 LEU cc_start: 0.8810 (tt) cc_final: 0.8547 (tt) REVERT: 0 48 SER cc_start: 0.9092 (p) cc_final: 0.8891 (m) REVERT: 0 53 GLU cc_start: 0.8067 (tp30) cc_final: 0.7553 (mm-30) REVERT: 0 158 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7431 (mm-30) REVERT: 0 353 ARG cc_start: 0.7405 (mpp80) cc_final: 0.6932 (mpp80) REVERT: 0 356 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7007 (tm-30) REVERT: 0 374 TYR cc_start: 0.8313 (m-10) cc_final: 0.8023 (m-80) REVERT: 0 394 CYS cc_start: 0.8704 (m) cc_final: 0.8276 (m) REVERT: 0 445 PHE cc_start: 0.6623 (p90) cc_final: 0.5354 (m-10) REVERT: 0 456 LYS cc_start: 0.8601 (mmpt) cc_final: 0.7858 (mtmt) REVERT: 0 478 LYS cc_start: 0.6843 (mtmt) cc_final: 0.6077 (mmtp) REVERT: 2 34 MET cc_start: 0.7467 (tmm) cc_final: 0.7009 (tmm) REVERT: 2 90 LEU cc_start: 0.6966 (mm) cc_final: 0.6632 (mm) REVERT: 2 113 THR cc_start: 0.8768 (p) cc_final: 0.8230 (t) REVERT: 2 231 GLN cc_start: 0.7783 (pt0) cc_final: 0.7540 (pt0) REVERT: 2 307 LYS cc_start: 0.8554 (ptmt) cc_final: 0.7855 (ptmm) REVERT: 2 318 MET cc_start: 0.8630 (mtp) cc_final: 0.8044 (mtp) REVERT: 2 486 GLU cc_start: 0.4894 (tm-30) cc_final: 0.4658 (tm-30) REVERT: 2 608 MET cc_start: 0.6271 (mmp) cc_final: 0.5836 (mmm) REVERT: 3 70 GLU cc_start: 0.7407 (pt0) cc_final: 0.7174 (pt0) REVERT: 3 118 ILE cc_start: 0.8720 (pt) cc_final: 0.8483 (pt) REVERT: 3 146 LEU cc_start: 0.8136 (tp) cc_final: 0.7870 (tp) REVERT: 3 180 MET cc_start: 0.7619 (mmm) cc_final: 0.7376 (mmm) REVERT: 3 202 ILE cc_start: 0.8910 (mt) cc_final: 0.8575 (mt) REVERT: 3 205 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8020 (tm-30) REVERT: 3 206 ILE cc_start: 0.8984 (mt) cc_final: 0.8406 (mt) REVERT: 3 227 PHE cc_start: 0.6942 (m-80) cc_final: 0.6717 (m-10) REVERT: 3 392 ILE cc_start: 0.8511 (mt) cc_final: 0.8256 (mt) REVERT: 3 489 LYS cc_start: 0.8697 (pttm) cc_final: 0.8319 (pptt) REVERT: 3 491 MET cc_start: 0.6459 (mtt) cc_final: 0.5716 (ppp) REVERT: 4 70 GLU cc_start: 0.7802 (pt0) cc_final: 0.7243 (pt0) REVERT: 4 113 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7494 (tm-30) REVERT: 4 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.7975 (tm-30) REVERT: 4 152 ASP cc_start: 0.7738 (t0) cc_final: 0.7175 (p0) REVERT: 4 290 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6284 (pt0) REVERT: 4 336 GLU cc_start: 0.8182 (tt0) cc_final: 0.7908 (tt0) REVERT: 4 340 ARG cc_start: 0.7565 (ptt90) cc_final: 0.7101 (ptt90) REVERT: 4 356 MET cc_start: 0.7961 (mtm) cc_final: 0.7707 (mtm) REVERT: 5 61 ASP cc_start: 0.7900 (p0) cc_final: 0.7601 (p0) REVERT: 5 119 LEU cc_start: 0.8834 (tp) cc_final: 0.8536 (tp) REVERT: 5 202 ILE cc_start: 0.9105 (mt) cc_final: 0.8846 (mt) REVERT: 5 244 PHE cc_start: 0.8279 (m-10) cc_final: 0.8014 (m-10) REVERT: 5 254 MET cc_start: 0.6877 (pmm) cc_final: 0.6594 (mtt) REVERT: 5 478 ASP cc_start: 0.8196 (m-30) cc_final: 0.7985 (m-30) REVERT: 7 23 LEU cc_start: 0.7687 (tp) cc_final: 0.7344 (tt) REVERT: 7 56 MET cc_start: 0.7502 (tpp) cc_final: 0.7299 (tpp) REVERT: 7 112 TYR cc_start: 0.5444 (t80) cc_final: 0.5126 (t80) REVERT: 7 211 ILE cc_start: 0.6114 (mt) cc_final: 0.4081 (mt) REVERT: 8 54 MET cc_start: 0.8068 (mpp) cc_final: 0.7361 (mpp) REVERT: 8 72 MET cc_start: 0.8303 (mtm) cc_final: 0.7675 (tpt) REVERT: 8 97 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7647 (tm-30) REVERT: 8 167 ILE cc_start: 0.8519 (mp) cc_final: 0.8246 (mt) REVERT: 8 185 ASN cc_start: 0.8845 (p0) cc_final: 0.8553 (p0) REVERT: 9 154 MET cc_start: 0.8292 (mmp) cc_final: 0.7790 (mmt) REVERT: 9 197 GLU cc_start: 0.8199 (mp0) cc_final: 0.7917 (mp0) REVERT: Q 132 MET cc_start: 0.7122 (mtt) cc_final: 0.6272 (mtp) REVERT: R 21 LYS cc_start: 0.5018 (mmmm) cc_final: 0.4732 (pptt) REVERT: R 41 GLN cc_start: 0.8298 (pp30) cc_final: 0.8053 (pp30) REVERT: R 58 LYS cc_start: 0.5894 (mttt) cc_final: 0.5640 (mttm) REVERT: R 113 ASN cc_start: 0.8490 (m110) cc_final: 0.8259 (m110) REVERT: T 16 LYS cc_start: 0.8120 (mttt) cc_final: 0.7009 (tttp) REVERT: X 51 THR cc_start: 0.8284 (m) cc_final: 0.8065 (t) REVERT: 6 82 ASP cc_start: 0.5399 (t0) cc_final: 0.5038 (m-30) REVERT: 6 109 MET cc_start: 0.7690 (tmm) cc_final: 0.6549 (ttm) REVERT: 6 301 ARG cc_start: 0.6554 (ttm170) cc_final: 0.6244 (ttm170) REVERT: 6 302 VAL cc_start: 0.8026 (p) cc_final: 0.7434 (p) REVERT: 6 338 LEU cc_start: 0.6648 (mt) cc_final: 0.6160 (mt) REVERT: 6 341 HIS cc_start: 0.6687 (p90) cc_final: 0.5478 (m90) REVERT: U 65 MET cc_start: 0.6523 (ppp) cc_final: 0.5357 (mtt) REVERT: U 96 MET cc_start: 0.1543 (ptm) cc_final: 0.0473 (mmt) REVERT: U 140 MET cc_start: 0.7758 (ttt) cc_final: 0.7535 (ptt) REVERT: U 147 LYS cc_start: 0.6300 (mmmm) cc_final: 0.5801 (tptt) REVERT: U 156 MET cc_start: 0.6646 (ptm) cc_final: 0.6345 (ptt) REVERT: U 216 PHE cc_start: 0.6818 (m-80) cc_final: 0.6398 (m-10) REVERT: U 234 LYS cc_start: 0.6229 (tttt) cc_final: 0.5552 (mptt) REVERT: U 321 LEU cc_start: 0.8015 (mm) cc_final: 0.7637 (mt) REVERT: U 324 GLN cc_start: 0.7506 (mp10) cc_final: 0.7086 (mp10) REVERT: U 383 LEU cc_start: 0.6643 (mt) cc_final: 0.5637 (mt) REVERT: U 418 VAL cc_start: 0.7966 (m) cc_final: 0.7450 (p) REVERT: U 434 LYS cc_start: 0.5554 (pttm) cc_final: 0.5024 (tptt) REVERT: d 7 LEU cc_start: 0.6796 (mt) cc_final: 0.6495 (pt) REVERT: d 38 GLN cc_start: 0.6541 (mm-40) cc_final: 0.5661 (mt0) REVERT: d 75 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8032 (mmmt) REVERT: d 84 HIS cc_start: 0.7980 (t-90) cc_final: 0.7595 (t-170) REVERT: d 128 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8512 (mptt) REVERT: d 165 GLN cc_start: 0.7262 (tt0) cc_final: 0.6174 (tp40) REVERT: d 175 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7104 (tt0) REVERT: d 176 MET cc_start: 0.6607 (mtm) cc_final: 0.5886 (ptp) REVERT: d 189 TYR cc_start: 0.7274 (t80) cc_final: 0.6523 (t80) REVERT: d 262 GLU cc_start: 0.6920 (tp30) cc_final: 0.5992 (mt-10) REVERT: d 346 ASN cc_start: 0.7084 (t0) cc_final: 0.6808 (t0) REVERT: d 349 PRO cc_start: 0.7726 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8508 (tptm) cc_final: 0.8061 (tptp) REVERT: a 61 MET cc_start: 0.8036 (mtp) cc_final: 0.7450 (mtt) REVERT: a 66 ARG cc_start: 0.8197 (mpt180) cc_final: 0.7871 (mmt-90) REVERT: a 124 GLU cc_start: 0.6423 (tp30) cc_final: 0.5224 (pp20) REVERT: a 125 LEU cc_start: 0.6382 (mt) cc_final: 0.5927 (mt) REVERT: a 128 LEU cc_start: 0.7833 (tp) cc_final: 0.7632 (tp) REVERT: a 290 LEU cc_start: 0.7910 (mt) cc_final: 0.7400 (tt) REVERT: a 383 ASN cc_start: 0.8875 (t0) cc_final: 0.8535 (m-40) REVERT: a 470 ILE cc_start: 0.6872 (mt) cc_final: 0.6667 (mt) REVERT: a 547 MET cc_start: 0.7904 (ttp) cc_final: 0.7602 (ttp) REVERT: a 565 PHE cc_start: 0.7321 (m-80) cc_final: 0.6968 (m-80) REVERT: a 587 MET cc_start: 0.4360 (ptm) cc_final: 0.4136 (ptp) REVERT: a 610 SER cc_start: 0.7900 (t) cc_final: 0.7606 (m) REVERT: a 623 MET cc_start: 0.8421 (ttp) cc_final: 0.8135 (tpp) REVERT: a 624 PHE cc_start: 0.8237 (m-80) cc_final: 0.8036 (m-80) REVERT: a 635 MET cc_start: 0.4500 (mmt) cc_final: 0.3773 (tpt) REVERT: a 740 TYR cc_start: 0.8365 (m-80) cc_final: 0.7627 (m-80) REVERT: a 769 ARG cc_start: 0.5502 (mtm180) cc_final: 0.4707 (mmt180) REVERT: e 40 MET cc_start: 0.6675 (tmm) cc_final: 0.6307 (ptm) REVERT: c 317 PHE cc_start: 0.1586 (m-80) cc_final: 0.1369 (m-80) REVERT: c 363 PHE cc_start: 0.6265 (t80) cc_final: 0.5673 (t80) REVERT: c 376 ASN cc_start: 0.7481 (m110) cc_final: 0.7103 (m110) REVERT: c 394 GLN cc_start: 0.7865 (mm110) cc_final: 0.7369 (mm110) outliers start: 2 outliers final: 0 residues processed: 1906 average time/residue: 0.5775 time to fit residues: 1896.4068 Evaluate side-chains 1649 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1649 time to evaluate : 5.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 495 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 478 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 509 optimal weight: 0.0870 chunk 545 optimal weight: 5.9990 chunk 395 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 629 optimal weight: 6.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN l 7 ASN ** 1 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 242 GLN ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 209 GLN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 358 ASN 7 85 GLN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN R 10 GLN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 113 ASN 6 23 HIS 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 HIS U 442 HIS U 443 HIS ** U 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN a 269 ASN a 494 GLN a 669 GLN a 725 HIS ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 66820 Z= 0.182 Angle : 0.606 14.758 90305 Z= 0.313 Chirality : 0.042 0.288 10236 Planarity : 0.004 0.107 11580 Dihedral : 4.381 76.836 9108 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 8319 helix: 1.68 (0.08), residues: 4684 sheet: 0.17 (0.21), residues: 684 loop : -1.33 (0.12), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP U 376 HIS 0.008 0.001 HIS U 259 PHE 0.050 0.002 PHE c 433 TYR 0.048 0.001 TYR g 68 ARG 0.010 0.000 ARG 4 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1893 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1891 time to evaluate : 5.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8946 (pt) cc_final: 0.8682 (tp) REVERT: b 89 LYS cc_start: 0.7174 (tttt) cc_final: 0.6131 (tppt) REVERT: b 146 LEU cc_start: 0.8765 (mm) cc_final: 0.8027 (mp) REVERT: b 157 ILE cc_start: 0.8960 (tt) cc_final: 0.8478 (tt) REVERT: b 168 GLN cc_start: 0.6867 (pp30) cc_final: 0.6625 (pp30) REVERT: b 173 PHE cc_start: 0.7298 (t80) cc_final: 0.6808 (t80) REVERT: g 61 MET cc_start: 0.8164 (mmm) cc_final: 0.7776 (ttp) REVERT: h 28 MET cc_start: 0.6780 (mmm) cc_final: 0.6344 (mmp) REVERT: h 51 LEU cc_start: 0.7277 (mt) cc_final: 0.7050 (mt) REVERT: h 54 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6926 (mtpt) REVERT: h 57 ILE cc_start: 0.7173 (mm) cc_final: 0.6768 (mm) REVERT: h 61 MET cc_start: 0.8428 (mtp) cc_final: 0.7805 (mmm) REVERT: h 126 ARG cc_start: 0.7505 (ttt180) cc_final: 0.6167 (tpt90) REVERT: h 144 TYR cc_start: 0.8554 (m-10) cc_final: 0.8251 (m-10) REVERT: i 23 MET cc_start: 0.6456 (ttm) cc_final: 0.6025 (ttm) REVERT: i 68 TYR cc_start: 0.8154 (m-80) cc_final: 0.7610 (m-80) REVERT: i 84 ILE cc_start: 0.5164 (tt) cc_final: 0.4808 (pt) REVERT: i 155 LYS cc_start: 0.5580 (mmtt) cc_final: 0.5150 (mmmt) REVERT: j 28 MET cc_start: 0.8718 (mtp) cc_final: 0.8515 (mtp) REVERT: j 51 LEU cc_start: 0.8178 (pp) cc_final: 0.7172 (tt) REVERT: j 84 ILE cc_start: 0.6393 (mm) cc_final: 0.6110 (mm) REVERT: k 28 MET cc_start: 0.6211 (ttt) cc_final: 0.5867 (ptm) REVERT: l 14 PHE cc_start: 0.7501 (m-10) cc_final: 0.7122 (m-80) REVERT: l 51 LEU cc_start: 0.6395 (mp) cc_final: 0.6150 (mp) REVERT: l 61 MET cc_start: 0.1798 (mtp) cc_final: 0.1359 (mtp) REVERT: l 92 GLN cc_start: 0.7012 (mm-40) cc_final: 0.6668 (mm-40) REVERT: l 121 THR cc_start: 0.5717 (m) cc_final: 0.5387 (m) REVERT: l 131 MET cc_start: 0.7176 (ttp) cc_final: 0.6814 (ttp) REVERT: m 90 PHE cc_start: 0.4557 (m-80) cc_final: 0.4340 (m-80) REVERT: n 28 MET cc_start: 0.6406 (mtp) cc_final: 0.6163 (tmm) REVERT: n 61 MET cc_start: 0.6908 (mmm) cc_final: 0.6575 (mmm) REVERT: n 70 LEU cc_start: 0.7258 (mt) cc_final: 0.6974 (mt) REVERT: n 86 LEU cc_start: 0.7019 (tp) cc_final: 0.6132 (tp) REVERT: n 127 LEU cc_start: 0.7089 (mm) cc_final: 0.6510 (pt) REVERT: o 70 LEU cc_start: 0.8858 (mt) cc_final: 0.8582 (mt) REVERT: o 144 TYR cc_start: 0.8112 (m-80) cc_final: 0.7755 (m-80) REVERT: 1 86 LEU cc_start: 0.8310 (tp) cc_final: 0.7651 (tp) REVERT: 1 205 MET cc_start: 0.8017 (ptt) cc_final: 0.7794 (ptp) REVERT: 1 232 ARG cc_start: 0.7091 (mtm-85) cc_final: 0.6202 (mtm-85) REVERT: 1 279 GLU cc_start: 0.7157 (pm20) cc_final: 0.5432 (mm-30) REVERT: 1 328 TYR cc_start: 0.7791 (m-10) cc_final: 0.7201 (m-80) REVERT: 1 495 LEU cc_start: 0.7809 (tp) cc_final: 0.7385 (pp) REVERT: 0 48 SER cc_start: 0.9080 (p) cc_final: 0.8854 (m) REVERT: 0 53 GLU cc_start: 0.8228 (tp30) cc_final: 0.7841 (tp30) REVERT: 0 163 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7334 (mmmt) REVERT: 0 306 MET cc_start: 0.8326 (mtm) cc_final: 0.7928 (mtt) REVERT: 0 356 GLU cc_start: 0.7871 (mt-10) cc_final: 0.6888 (tm-30) REVERT: 0 374 TYR cc_start: 0.8246 (m-10) cc_final: 0.8013 (m-80) REVERT: 0 394 CYS cc_start: 0.8770 (m) cc_final: 0.8413 (m) REVERT: 0 445 PHE cc_start: 0.6606 (p90) cc_final: 0.5374 (m-10) REVERT: 0 456 LYS cc_start: 0.8539 (mmpt) cc_final: 0.7845 (mtmt) REVERT: 0 478 LYS cc_start: 0.6730 (mtmt) cc_final: 0.6071 (mmtp) REVERT: 2 34 MET cc_start: 0.7499 (tmm) cc_final: 0.7021 (tmm) REVERT: 2 113 THR cc_start: 0.8804 (p) cc_final: 0.8312 (t) REVERT: 2 231 GLN cc_start: 0.7786 (pt0) cc_final: 0.7483 (pt0) REVERT: 2 318 MET cc_start: 0.8443 (mtp) cc_final: 0.7821 (mtp) REVERT: 2 476 ARG cc_start: 0.8045 (tmt170) cc_final: 0.7219 (ttp-170) REVERT: 2 608 MET cc_start: 0.6284 (mmp) cc_final: 0.5907 (mmp) REVERT: 3 105 ILE cc_start: 0.8603 (mt) cc_final: 0.8323 (mt) REVERT: 3 118 ILE cc_start: 0.8711 (pt) cc_final: 0.8460 (pt) REVERT: 3 146 LEU cc_start: 0.8343 (tp) cc_final: 0.7962 (tp) REVERT: 3 202 ILE cc_start: 0.8822 (mt) cc_final: 0.8509 (mt) REVERT: 3 205 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7842 (tm-30) REVERT: 3 206 ILE cc_start: 0.8998 (mt) cc_final: 0.8412 (mt) REVERT: 3 266 ASP cc_start: 0.9095 (m-30) cc_final: 0.8775 (m-30) REVERT: 3 377 ILE cc_start: 0.8114 (mm) cc_final: 0.7864 (mm) REVERT: 3 392 ILE cc_start: 0.8496 (mt) cc_final: 0.8261 (mt) REVERT: 3 489 LYS cc_start: 0.8676 (pttm) cc_final: 0.8284 (pptt) REVERT: 3 491 MET cc_start: 0.6497 (mtt) cc_final: 0.5752 (ppp) REVERT: 4 68 TYR cc_start: 0.8314 (t80) cc_final: 0.8043 (t80) REVERT: 4 70 GLU cc_start: 0.7790 (pt0) cc_final: 0.7215 (pt0) REVERT: 4 113 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7495 (tm-30) REVERT: 4 148 GLU cc_start: 0.8295 (tt0) cc_final: 0.7959 (tm-30) REVERT: 4 152 ASP cc_start: 0.7782 (t0) cc_final: 0.7093 (p0) REVERT: 4 265 ASN cc_start: 0.8683 (m-40) cc_final: 0.8185 (m-40) REVERT: 4 290 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6305 (pt0) REVERT: 4 340 ARG cc_start: 0.7410 (ptt90) cc_final: 0.7065 (ptt90) REVERT: 4 356 MET cc_start: 0.8016 (mtm) cc_final: 0.7727 (mtm) REVERT: 5 61 ASP cc_start: 0.7856 (p0) cc_final: 0.7578 (p0) REVERT: 5 119 LEU cc_start: 0.8815 (tp) cc_final: 0.8507 (tp) REVERT: 5 202 ILE cc_start: 0.9031 (mt) cc_final: 0.8818 (mt) REVERT: 5 208 ARG cc_start: 0.7943 (ptp90) cc_final: 0.7382 (ptp90) REVERT: 5 238 MET cc_start: 0.7708 (mmp) cc_final: 0.7378 (mmp) REVERT: 5 244 PHE cc_start: 0.8225 (m-10) cc_final: 0.7941 (m-10) REVERT: 5 254 MET cc_start: 0.6942 (pmm) cc_final: 0.6732 (mtt) REVERT: 5 350 GLN cc_start: 0.8056 (tp40) cc_final: 0.7830 (tp-100) REVERT: 5 478 ASP cc_start: 0.8201 (m-30) cc_final: 0.7980 (m-30) REVERT: 7 23 LEU cc_start: 0.7642 (tp) cc_final: 0.7366 (tt) REVERT: 7 56 MET cc_start: 0.7489 (tpp) cc_final: 0.7286 (tpp) REVERT: 7 91 GLN cc_start: 0.7323 (tt0) cc_final: 0.7120 (tt0) REVERT: 7 112 TYR cc_start: 0.5487 (t80) cc_final: 0.5240 (t80) REVERT: 7 211 ILE cc_start: 0.6116 (mt) cc_final: 0.4105 (mt) REVERT: 8 16 MET cc_start: 0.6778 (ttp) cc_final: 0.6567 (tmm) REVERT: 8 28 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8135 (tm-30) REVERT: 8 50 ARG cc_start: 0.6376 (mmp80) cc_final: 0.5719 (mmp80) REVERT: 8 54 MET cc_start: 0.8020 (mpp) cc_final: 0.7365 (mpp) REVERT: 8 72 MET cc_start: 0.8375 (mtm) cc_final: 0.7702 (tpt) REVERT: 8 97 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7578 (tm-30) REVERT: 8 185 ASN cc_start: 0.8833 (p0) cc_final: 0.8528 (p0) REVERT: 9 154 MET cc_start: 0.8291 (mmp) cc_final: 0.7763 (mmt) REVERT: 9 197 GLU cc_start: 0.8185 (mp0) cc_final: 0.7791 (mp0) REVERT: Q 132 MET cc_start: 0.7172 (mtt) cc_final: 0.6249 (mtp) REVERT: R 58 LYS cc_start: 0.5938 (mttt) cc_final: 0.5702 (mttm) REVERT: R 113 ASN cc_start: 0.8491 (m110) cc_final: 0.8275 (m110) REVERT: T 16 LYS cc_start: 0.8064 (mttt) cc_final: 0.6937 (tttp) REVERT: T 34 LYS cc_start: 0.8038 (tppt) cc_final: 0.7243 (mttt) REVERT: 6 82 ASP cc_start: 0.5376 (t0) cc_final: 0.5006 (m-30) REVERT: 6 109 MET cc_start: 0.7673 (tmm) cc_final: 0.6606 (ttm) REVERT: 6 151 GLN cc_start: 0.6914 (mp-120) cc_final: 0.5934 (pt0) REVERT: 6 301 ARG cc_start: 0.6484 (ttm170) cc_final: 0.6212 (ttm170) REVERT: 6 338 LEU cc_start: 0.6676 (mt) cc_final: 0.6142 (mt) REVERT: 6 341 HIS cc_start: 0.6753 (p90) cc_final: 0.5649 (m90) REVERT: U 65 MET cc_start: 0.6517 (ppp) cc_final: 0.5358 (mtt) REVERT: U 96 MET cc_start: 0.1515 (ptm) cc_final: 0.0530 (mmt) REVERT: U 140 MET cc_start: 0.8005 (ttt) cc_final: 0.7731 (ptt) REVERT: U 147 LYS cc_start: 0.6328 (mmmm) cc_final: 0.5784 (tptt) REVERT: U 156 MET cc_start: 0.6873 (ptm) cc_final: 0.6566 (ptt) REVERT: U 199 GLN cc_start: 0.7012 (mm110) cc_final: 0.6431 (tm-30) REVERT: U 234 LYS cc_start: 0.6457 (tttt) cc_final: 0.5724 (mptt) REVERT: U 256 MET cc_start: 0.5875 (mmm) cc_final: 0.5471 (mmm) REVERT: U 293 LEU cc_start: 0.8137 (mm) cc_final: 0.7831 (mp) REVERT: U 309 MET cc_start: 0.4907 (mtt) cc_final: 0.4351 (mtp) REVERT: U 321 LEU cc_start: 0.8046 (mm) cc_final: 0.7709 (mt) REVERT: U 324 GLN cc_start: 0.7575 (mp10) cc_final: 0.7180 (mp10) REVERT: U 383 LEU cc_start: 0.6400 (mt) cc_final: 0.5508 (mt) REVERT: U 418 VAL cc_start: 0.7757 (m) cc_final: 0.7288 (p) REVERT: U 434 LYS cc_start: 0.5498 (pttm) cc_final: 0.4999 (tptt) REVERT: U 460 MET cc_start: 0.6526 (tpp) cc_final: 0.5789 (tpp) REVERT: d 38 GLN cc_start: 0.6582 (mm-40) cc_final: 0.5723 (mt0) REVERT: d 71 ASP cc_start: 0.6694 (t70) cc_final: 0.6421 (t0) REVERT: d 75 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7978 (mmmt) REVERT: d 84 HIS cc_start: 0.7918 (t-90) cc_final: 0.7535 (t-170) REVERT: d 128 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8423 (mptt) REVERT: d 165 GLN cc_start: 0.7245 (tt0) cc_final: 0.6122 (tp40) REVERT: d 186 TYR cc_start: 0.6545 (t80) cc_final: 0.6189 (t80) REVERT: d 189 TYR cc_start: 0.7150 (t80) cc_final: 0.6344 (t80) REVERT: d 262 GLU cc_start: 0.6898 (tp30) cc_final: 0.6010 (mt-10) REVERT: d 346 ASN cc_start: 0.7028 (t0) cc_final: 0.6693 (t0) REVERT: d 349 PRO cc_start: 0.7707 (Cg_endo) cc_final: 0.7381 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8529 (tptm) cc_final: 0.8057 (tptp) REVERT: a 61 MET cc_start: 0.8046 (mtp) cc_final: 0.7651 (mtt) REVERT: a 124 GLU cc_start: 0.6474 (tp30) cc_final: 0.5356 (pp20) REVERT: a 125 LEU cc_start: 0.6372 (mt) cc_final: 0.5982 (mt) REVERT: a 290 LEU cc_start: 0.7963 (mt) cc_final: 0.7574 (tp) REVERT: a 383 ASN cc_start: 0.8808 (t0) cc_final: 0.8531 (m-40) REVERT: a 547 MET cc_start: 0.7846 (ttp) cc_final: 0.7574 (ttp) REVERT: a 565 PHE cc_start: 0.7303 (m-80) cc_final: 0.6950 (m-80) REVERT: a 610 SER cc_start: 0.7977 (t) cc_final: 0.7757 (m) REVERT: a 623 MET cc_start: 0.8462 (ttp) cc_final: 0.8146 (tpp) REVERT: a 635 MET cc_start: 0.4472 (mmt) cc_final: 0.3990 (tpt) REVERT: a 740 TYR cc_start: 0.8315 (m-80) cc_final: 0.7600 (m-80) REVERT: a 769 ARG cc_start: 0.5529 (mtm180) cc_final: 0.4696 (mmt180) REVERT: e 57 LEU cc_start: 0.8047 (mt) cc_final: 0.7750 (mt) REVERT: c 376 ASN cc_start: 0.7549 (m110) cc_final: 0.7303 (m-40) outliers start: 2 outliers final: 0 residues processed: 1892 average time/residue: 0.5906 time to fit residues: 1931.4979 Evaluate side-chains 1635 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1635 time to evaluate : 5.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 728 optimal weight: 4.9990 chunk 767 optimal weight: 0.7980 chunk 700 optimal weight: 3.9990 chunk 746 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 325 optimal weight: 10.0000 chunk 586 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 674 optimal weight: 7.9990 chunk 705 optimal weight: 0.3980 chunk 743 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 92 GLN l 92 GLN m 123 GLN 1 65 GLN ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 397 ASN 0 430 GLN ** 0 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 207 GLN ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 111 HIS ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN 8 206 GLN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN 6 23 HIS 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 296 HIS U 131 ASN ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 13 ASN ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 ASN a 48 GLN a 269 ASN a 669 GLN ** a 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 66820 Z= 0.270 Angle : 0.672 12.679 90305 Z= 0.350 Chirality : 0.044 0.289 10236 Planarity : 0.005 0.114 11580 Dihedral : 4.639 76.934 9108 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 0.08 % Allowed : 0.85 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 8319 helix: 1.38 (0.08), residues: 4703 sheet: 0.01 (0.21), residues: 691 loop : -1.51 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP 2 450 HIS 0.009 0.001 HIS U 443 PHE 0.040 0.002 PHE b 150 TYR 0.053 0.002 TYR g 68 ARG 0.014 0.001 ARG Q 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1842 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1836 time to evaluate : 5.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8940 (pt) cc_final: 0.8665 (tp) REVERT: b 146 LEU cc_start: 0.8680 (mm) cc_final: 0.7925 (mp) REVERT: b 168 GLN cc_start: 0.6919 (pp30) cc_final: 0.6660 (pp30) REVERT: g 28 MET cc_start: 0.8918 (mtp) cc_final: 0.8523 (mtt) REVERT: g 47 MET cc_start: 0.7578 (mmm) cc_final: 0.7341 (mmm) REVERT: g 61 MET cc_start: 0.8103 (mmm) cc_final: 0.7543 (ttp) REVERT: g 90 PHE cc_start: 0.6984 (m-10) cc_final: 0.6766 (m-10) REVERT: h 28 MET cc_start: 0.6803 (mmm) cc_final: 0.6334 (mmp) REVERT: h 51 LEU cc_start: 0.7281 (mt) cc_final: 0.7036 (mt) REVERT: h 57 ILE cc_start: 0.7296 (mm) cc_final: 0.6867 (mm) REVERT: h 61 MET cc_start: 0.8474 (mtp) cc_final: 0.7881 (mmm) REVERT: h 126 ARG cc_start: 0.7573 (ttt180) cc_final: 0.5892 (tpt90) REVERT: h 144 TYR cc_start: 0.8605 (m-10) cc_final: 0.8267 (m-10) REVERT: i 23 MET cc_start: 0.6338 (ttm) cc_final: 0.5915 (ttm) REVERT: i 68 TYR cc_start: 0.8282 (m-80) cc_final: 0.7670 (m-80) REVERT: i 84 ILE cc_start: 0.5167 (tt) cc_final: 0.4840 (pt) REVERT: i 131 MET cc_start: 0.5881 (ppp) cc_final: 0.5179 (mtp) REVERT: i 155 LYS cc_start: 0.5527 (mmtt) cc_final: 0.5082 (mmmt) REVERT: j 28 MET cc_start: 0.8781 (mtp) cc_final: 0.8557 (mtp) REVERT: j 51 LEU cc_start: 0.8178 (pp) cc_final: 0.7179 (tt) REVERT: j 84 ILE cc_start: 0.6411 (mm) cc_final: 0.6135 (mm) REVERT: k 28 MET cc_start: 0.6214 (ttt) cc_final: 0.5880 (ptm) REVERT: l 51 LEU cc_start: 0.6569 (mp) cc_final: 0.6312 (mp) REVERT: l 61 MET cc_start: 0.1922 (mtp) cc_final: 0.1529 (mtp) REVERT: l 121 THR cc_start: 0.5457 (m) cc_final: 0.5229 (m) REVERT: l 131 MET cc_start: 0.7247 (ttp) cc_final: 0.6909 (ttp) REVERT: m 23 MET cc_start: 0.4070 (tpt) cc_final: 0.3344 (tpt) REVERT: m 61 MET cc_start: 0.8368 (ttt) cc_final: 0.8120 (ttt) REVERT: n 61 MET cc_start: 0.6910 (mmm) cc_final: 0.6616 (mmm) REVERT: n 70 LEU cc_start: 0.7186 (mt) cc_final: 0.6792 (mt) REVERT: n 86 LEU cc_start: 0.6735 (tp) cc_final: 0.5919 (tp) REVERT: o 32 TYR cc_start: 0.8400 (t80) cc_final: 0.8117 (t80) REVERT: o 70 LEU cc_start: 0.8803 (mt) cc_final: 0.8088 (mt) REVERT: 1 86 LEU cc_start: 0.8445 (tp) cc_final: 0.7660 (tp) REVERT: 1 205 MET cc_start: 0.7990 (ptt) cc_final: 0.7746 (ptp) REVERT: 1 241 VAL cc_start: 0.8145 (t) cc_final: 0.7889 (t) REVERT: 1 328 TYR cc_start: 0.7898 (m-10) cc_final: 0.7270 (m-80) REVERT: 1 346 MET cc_start: 0.8502 (tpt) cc_final: 0.8037 (tpt) REVERT: 0 340 MET cc_start: 0.7699 (mtp) cc_final: 0.7424 (mtp) REVERT: 0 356 GLU cc_start: 0.8007 (mt-10) cc_final: 0.6904 (tm-30) REVERT: 0 394 CYS cc_start: 0.8514 (m) cc_final: 0.8010 (m) REVERT: 0 425 THR cc_start: 0.8108 (m) cc_final: 0.7815 (m) REVERT: 0 445 PHE cc_start: 0.6316 (p90) cc_final: 0.5274 (m-80) REVERT: 0 457 TYR cc_start: 0.8248 (m-80) cc_final: 0.7598 (m-80) REVERT: 0 478 LYS cc_start: 0.6864 (mtmt) cc_final: 0.6100 (mmtp) REVERT: 0 543 ASN cc_start: 0.3287 (p0) cc_final: 0.2845 (m110) REVERT: 2 34 MET cc_start: 0.7519 (tmm) cc_final: 0.6999 (tmm) REVERT: 2 90 LEU cc_start: 0.6718 (mm) cc_final: 0.6472 (mm) REVERT: 2 113 THR cc_start: 0.8755 (p) cc_final: 0.8250 (t) REVERT: 2 274 TYR cc_start: 0.8417 (t80) cc_final: 0.7809 (t80) REVERT: 2 307 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8034 (ptmm) REVERT: 2 318 MET cc_start: 0.8418 (mtp) cc_final: 0.7830 (mtp) REVERT: 2 419 ASP cc_start: 0.6825 (m-30) cc_final: 0.6617 (m-30) REVERT: 2 476 ARG cc_start: 0.8014 (tmt170) cc_final: 0.7209 (ttp-170) REVERT: 2 608 MET cc_start: 0.6425 (mmp) cc_final: 0.5943 (mmm) REVERT: 3 67 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7244 (mmm160) REVERT: 3 70 GLU cc_start: 0.7182 (pt0) cc_final: 0.6919 (pt0) REVERT: 3 118 ILE cc_start: 0.8656 (pt) cc_final: 0.8426 (pt) REVERT: 3 146 LEU cc_start: 0.8448 (tp) cc_final: 0.8053 (tp) REVERT: 3 180 MET cc_start: 0.7786 (tpt) cc_final: 0.7391 (mmm) REVERT: 3 202 ILE cc_start: 0.8924 (mt) cc_final: 0.8692 (mt) REVERT: 3 266 ASP cc_start: 0.9095 (m-30) cc_final: 0.8822 (m-30) REVERT: 3 377 ILE cc_start: 0.8195 (mm) cc_final: 0.7928 (mm) REVERT: 3 392 ILE cc_start: 0.8543 (mt) cc_final: 0.8289 (mt) REVERT: 3 489 LYS cc_start: 0.8742 (pttm) cc_final: 0.8327 (pptt) REVERT: 3 491 MET cc_start: 0.6491 (mtt) cc_final: 0.5649 (ppp) REVERT: 4 68 TYR cc_start: 0.8428 (t80) cc_final: 0.8182 (t80) REVERT: 4 70 GLU cc_start: 0.7875 (pt0) cc_final: 0.7350 (pt0) REVERT: 4 113 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7451 (tm-30) REVERT: 4 148 GLU cc_start: 0.8391 (tt0) cc_final: 0.7997 (tm-30) REVERT: 4 152 ASP cc_start: 0.7716 (t0) cc_final: 0.7136 (p0) REVERT: 4 265 ASN cc_start: 0.8646 (m-40) cc_final: 0.8136 (m-40) REVERT: 4 290 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6271 (pt0) REVERT: 4 340 ARG cc_start: 0.7437 (ptt90) cc_final: 0.7142 (ptt90) REVERT: 4 356 MET cc_start: 0.7953 (mtm) cc_final: 0.7703 (mtm) REVERT: 4 377 ILE cc_start: 0.8679 (mm) cc_final: 0.8388 (mm) REVERT: 5 61 ASP cc_start: 0.7899 (p0) cc_final: 0.7586 (p0) REVERT: 5 67 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7330 (mtp85) REVERT: 5 100 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7340 (tm-30) REVERT: 5 102 THR cc_start: 0.8115 (p) cc_final: 0.7893 (p) REVERT: 5 119 LEU cc_start: 0.8848 (tp) cc_final: 0.8524 (tp) REVERT: 5 244 PHE cc_start: 0.8244 (m-10) cc_final: 0.7871 (m-10) REVERT: 5 254 MET cc_start: 0.7107 (pmm) cc_final: 0.6808 (mtt) REVERT: 5 350 GLN cc_start: 0.8083 (tp40) cc_final: 0.7812 (tp-100) REVERT: 5 478 ASP cc_start: 0.8202 (m-30) cc_final: 0.7959 (m-30) REVERT: 5 489 LYS cc_start: 0.7606 (pttt) cc_final: 0.6990 (tmmt) REVERT: 7 23 LEU cc_start: 0.7584 (tp) cc_final: 0.7274 (tt) REVERT: 7 56 MET cc_start: 0.7540 (tpp) cc_final: 0.7321 (tpp) REVERT: 7 112 TYR cc_start: 0.5449 (t80) cc_final: 0.5174 (t80) REVERT: 7 182 ARG cc_start: 0.5708 (mtm-85) cc_final: 0.4902 (tpm170) REVERT: 7 211 ILE cc_start: 0.6044 (mt) cc_final: 0.3919 (mt) REVERT: 8 28 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8211 (tm-30) REVERT: 8 54 MET cc_start: 0.8014 (mpp) cc_final: 0.7544 (mmp) REVERT: 8 72 MET cc_start: 0.8277 (mtm) cc_final: 0.7649 (tpt) REVERT: 8 97 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7770 (tm-30) REVERT: 8 185 ASN cc_start: 0.8856 (p0) cc_final: 0.8556 (p0) REVERT: 9 154 MET cc_start: 0.8360 (mmp) cc_final: 0.7818 (mmt) REVERT: 9 197 GLU cc_start: 0.8269 (mp0) cc_final: 0.7995 (mp0) REVERT: 9 206 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8085 (mt0) REVERT: Q 132 MET cc_start: 0.7070 (mtt) cc_final: 0.6263 (mtp) REVERT: R 41 GLN cc_start: 0.8378 (pp30) cc_final: 0.8163 (pp30) REVERT: R 113 ASN cc_start: 0.8606 (m110) cc_final: 0.8304 (m110) REVERT: T 16 LYS cc_start: 0.8127 (mttt) cc_final: 0.7017 (tttp) REVERT: T 34 LYS cc_start: 0.8046 (tppt) cc_final: 0.7226 (mttt) REVERT: V 102 MET cc_start: 0.6256 (ttt) cc_final: 0.5914 (ttp) REVERT: 6 82 ASP cc_start: 0.5506 (t0) cc_final: 0.5012 (m-30) REVERT: 6 109 MET cc_start: 0.7795 (tmm) cc_final: 0.6515 (mtt) REVERT: 6 301 ARG cc_start: 0.6579 (ttm170) cc_final: 0.6187 (ttm170) REVERT: 6 302 VAL cc_start: 0.8101 (p) cc_final: 0.7451 (p) REVERT: 6 338 LEU cc_start: 0.6624 (mt) cc_final: 0.6111 (mt) REVERT: 6 341 HIS cc_start: 0.6622 (p90) cc_final: 0.5381 (m90) REVERT: U 65 MET cc_start: 0.6533 (ppp) cc_final: 0.5373 (mtt) REVERT: U 96 MET cc_start: 0.1481 (ptm) cc_final: 0.0435 (mmt) REVERT: U 140 MET cc_start: 0.8060 (ttt) cc_final: 0.7796 (ptt) REVERT: U 147 LYS cc_start: 0.6465 (mmmm) cc_final: 0.5879 (tptt) REVERT: U 156 MET cc_start: 0.6942 (ptm) cc_final: 0.6625 (ptt) REVERT: U 234 LYS cc_start: 0.6508 (tttt) cc_final: 0.5569 (mptt) REVERT: U 363 ARG cc_start: 0.5827 (ttt180) cc_final: 0.5607 (mmt-90) REVERT: U 383 LEU cc_start: 0.6224 (mt) cc_final: 0.5448 (mt) REVERT: U 418 VAL cc_start: 0.7721 (m) cc_final: 0.7435 (t) REVERT: U 434 LYS cc_start: 0.5560 (pttm) cc_final: 0.5027 (tptt) REVERT: U 460 MET cc_start: 0.6612 (tpp) cc_final: 0.5876 (tpp) REVERT: d 38 GLN cc_start: 0.6665 (mm-40) cc_final: 0.5908 (mt0) REVERT: d 75 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8054 (mmmt) REVERT: d 165 GLN cc_start: 0.7136 (tt0) cc_final: 0.5809 (tp40) REVERT: d 175 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7090 (tt0) REVERT: d 186 TYR cc_start: 0.6651 (t80) cc_final: 0.6293 (t80) REVERT: d 189 TYR cc_start: 0.7302 (t80) cc_final: 0.6596 (t80) REVERT: d 346 ASN cc_start: 0.7175 (t0) cc_final: 0.6889 (t0) REVERT: d 349 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.7477 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8590 (tptm) cc_final: 0.8124 (tptp) REVERT: a 61 MET cc_start: 0.8036 (mtp) cc_final: 0.7423 (mtt) REVERT: a 124 GLU cc_start: 0.6659 (tp30) cc_final: 0.5438 (pp20) REVERT: a 125 LEU cc_start: 0.6441 (mt) cc_final: 0.5991 (mt) REVERT: a 290 LEU cc_start: 0.7970 (mt) cc_final: 0.7449 (tt) REVERT: a 383 ASN cc_start: 0.8859 (t0) cc_final: 0.8528 (m-40) REVERT: a 470 ILE cc_start: 0.6680 (mt) cc_final: 0.6467 (mt) REVERT: a 547 MET cc_start: 0.7875 (ttp) cc_final: 0.7643 (ttp) REVERT: a 565 PHE cc_start: 0.7318 (m-80) cc_final: 0.7044 (m-80) REVERT: a 598 ILE cc_start: 0.7541 (mt) cc_final: 0.7266 (mt) REVERT: a 610 SER cc_start: 0.7967 (t) cc_final: 0.7705 (m) REVERT: a 623 MET cc_start: 0.8465 (ttp) cc_final: 0.8207 (tpp) REVERT: a 624 PHE cc_start: 0.8227 (m-80) cc_final: 0.7947 (m-80) REVERT: a 635 MET cc_start: 0.4534 (mmt) cc_final: 0.3839 (tpt) REVERT: a 722 GLN cc_start: 0.7716 (tp40) cc_final: 0.7052 (tp40) REVERT: a 726 THR cc_start: 0.8033 (m) cc_final: 0.7578 (m) REVERT: a 740 TYR cc_start: 0.8376 (m-80) cc_final: 0.7788 (m-80) REVERT: a 769 ARG cc_start: 0.5587 (mtm180) cc_final: 0.4678 (mmt180) REVERT: e 57 LEU cc_start: 0.8023 (mt) cc_final: 0.7740 (mt) REVERT: c 376 ASN cc_start: 0.7294 (m110) cc_final: 0.6865 (m110) outliers start: 6 outliers final: 2 residues processed: 1841 average time/residue: 0.5783 time to fit residues: 1840.1220 Evaluate side-chains 1603 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1601 time to evaluate : 5.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 490 optimal weight: 6.9990 chunk 789 optimal weight: 6.9990 chunk 481 optimal weight: 0.5980 chunk 374 optimal weight: 0.2980 chunk 548 optimal weight: 5.9990 chunk 827 optimal weight: 8.9990 chunk 761 optimal weight: 5.9990 chunk 659 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 509 optimal weight: 0.0970 chunk 404 optimal weight: 0.8980 overall best weight: 1.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 397 ASN ** 0 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 573 HIS 0 603 GLN ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 456 GLN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 85 GLN ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 126 GLN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN 6 23 HIS 6 116 GLN ** 6 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 442 HIS ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN a 269 ASN a 669 GLN a 725 HIS ** a 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 308 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 66820 Z= 0.199 Angle : 0.640 15.518 90305 Z= 0.329 Chirality : 0.043 0.281 10236 Planarity : 0.004 0.112 11580 Dihedral : 4.517 77.005 9108 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8319 helix: 1.52 (0.08), residues: 4688 sheet: 0.14 (0.21), residues: 684 loop : -1.49 (0.11), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP 2 450 HIS 0.007 0.001 HIS a 725 PHE 0.053 0.002 PHE c 433 TYR 0.059 0.002 TYR o 144 ARG 0.015 0.001 ARG 5 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16638 Ramachandran restraints generated. 8319 Oldfield, 0 Emsley, 8319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1830 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1828 time to evaluate : 5.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 ILE cc_start: 0.8925 (pt) cc_final: 0.8673 (tp) REVERT: b 89 LYS cc_start: 0.6869 (tttt) cc_final: 0.5926 (tppt) REVERT: b 146 LEU cc_start: 0.8734 (mm) cc_final: 0.7956 (mp) REVERT: g 28 MET cc_start: 0.8894 (mtp) cc_final: 0.8489 (mtt) REVERT: g 47 MET cc_start: 0.7536 (mmm) cc_final: 0.7310 (mmm) REVERT: g 61 MET cc_start: 0.8001 (mmm) cc_final: 0.7393 (ttp) REVERT: h 13 PHE cc_start: 0.7354 (m-10) cc_final: 0.6893 (m-10) REVERT: h 28 MET cc_start: 0.6748 (mmm) cc_final: 0.6336 (mmp) REVERT: h 57 ILE cc_start: 0.7008 (mm) cc_final: 0.6603 (mm) REVERT: h 61 MET cc_start: 0.8431 (mtp) cc_final: 0.7825 (mmm) REVERT: h 126 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6158 (tmt170) REVERT: h 144 TYR cc_start: 0.8603 (m-10) cc_final: 0.8267 (m-10) REVERT: i 23 MET cc_start: 0.6291 (ttm) cc_final: 0.5907 (ttm) REVERT: i 68 TYR cc_start: 0.8270 (m-80) cc_final: 0.7646 (m-80) REVERT: i 84 ILE cc_start: 0.4805 (tt) cc_final: 0.4478 (pt) REVERT: i 155 LYS cc_start: 0.5422 (mmtt) cc_final: 0.4962 (mmmt) REVERT: j 28 MET cc_start: 0.8787 (mtp) cc_final: 0.8480 (mtp) REVERT: j 51 LEU cc_start: 0.8220 (pp) cc_final: 0.7261 (tt) REVERT: j 84 ILE cc_start: 0.6451 (mm) cc_final: 0.6165 (mm) REVERT: k 28 MET cc_start: 0.6183 (ttt) cc_final: 0.5879 (ptm) REVERT: l 24 VAL cc_start: 0.6688 (t) cc_final: 0.5775 (t) REVERT: l 51 LEU cc_start: 0.6537 (mp) cc_final: 0.6267 (mp) REVERT: l 61 MET cc_start: 0.1810 (mtp) cc_final: 0.1370 (mtp) REVERT: l 121 THR cc_start: 0.5259 (m) cc_final: 0.5012 (m) REVERT: l 131 MET cc_start: 0.7274 (ttp) cc_final: 0.6939 (ttp) REVERT: m 23 MET cc_start: 0.4060 (tpt) cc_final: 0.3425 (tpt) REVERT: m 61 MET cc_start: 0.8382 (ttt) cc_final: 0.8078 (ttt) REVERT: m 131 MET cc_start: 0.4673 (ptp) cc_final: 0.3867 (tmm) REVERT: m 132 ILE cc_start: 0.8521 (mt) cc_final: 0.7893 (mt) REVERT: n 61 MET cc_start: 0.6894 (mmm) cc_final: 0.6566 (mmm) REVERT: n 86 LEU cc_start: 0.6679 (tp) cc_final: 0.5815 (tp) REVERT: n 127 LEU cc_start: 0.7069 (mm) cc_final: 0.6538 (pt) REVERT: o 32 TYR cc_start: 0.8364 (t80) cc_final: 0.8110 (t80) REVERT: o 70 LEU cc_start: 0.8852 (mt) cc_final: 0.7784 (mt) REVERT: o 144 TYR cc_start: 0.7977 (m-80) cc_final: 0.7247 (m-80) REVERT: 1 86 LEU cc_start: 0.8001 (tp) cc_final: 0.7744 (tp) REVERT: 1 205 MET cc_start: 0.8120 (ptt) cc_final: 0.7838 (ptp) REVERT: 1 231 GLN cc_start: 0.7245 (pm20) cc_final: 0.6737 (pm20) REVERT: 1 232 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6303 (mtm-85) REVERT: 1 241 VAL cc_start: 0.8059 (t) cc_final: 0.7823 (t) REVERT: 1 328 TYR cc_start: 0.7750 (m-10) cc_final: 0.7162 (m-80) REVERT: 1 346 MET cc_start: 0.8288 (tpt) cc_final: 0.7997 (tpt) REVERT: 1 495 LEU cc_start: 0.7854 (tp) cc_final: 0.7394 (pp) REVERT: 1 550 MET cc_start: 0.6814 (mtp) cc_final: 0.6452 (mtp) REVERT: 0 163 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7333 (mmmt) REVERT: 0 306 MET cc_start: 0.8183 (mtm) cc_final: 0.7796 (mtt) REVERT: 0 356 GLU cc_start: 0.7839 (mt-10) cc_final: 0.6751 (tm-30) REVERT: 0 394 CYS cc_start: 0.8618 (m) cc_final: 0.8101 (m) REVERT: 0 445 PHE cc_start: 0.6445 (p90) cc_final: 0.5259 (m-80) REVERT: 0 456 LYS cc_start: 0.8584 (mmmt) cc_final: 0.7697 (mtmt) REVERT: 0 457 TYR cc_start: 0.8482 (m-80) cc_final: 0.7534 (m-80) REVERT: 0 478 LYS cc_start: 0.6724 (mtmt) cc_final: 0.6056 (mmtp) REVERT: 0 543 ASN cc_start: 0.3094 (p0) cc_final: 0.2518 (m110) REVERT: 2 34 MET cc_start: 0.7420 (tmm) cc_final: 0.6960 (tmm) REVERT: 2 90 LEU cc_start: 0.6767 (mm) cc_final: 0.6182 (mm) REVERT: 2 113 THR cc_start: 0.8739 (p) cc_final: 0.8266 (t) REVERT: 2 231 GLN cc_start: 0.7743 (pt0) cc_final: 0.7481 (pt0) REVERT: 2 274 TYR cc_start: 0.8417 (t80) cc_final: 0.7766 (t80) REVERT: 2 307 LYS cc_start: 0.8530 (ptmt) cc_final: 0.7912 (ptmm) REVERT: 2 318 MET cc_start: 0.8234 (mtp) cc_final: 0.7620 (mtp) REVERT: 2 454 TYR cc_start: 0.8036 (p90) cc_final: 0.7792 (p90) REVERT: 2 476 ARG cc_start: 0.7967 (tmt170) cc_final: 0.7670 (tpt90) REVERT: 2 486 GLU cc_start: 0.5694 (pp20) cc_final: 0.5455 (pp20) REVERT: 2 608 MET cc_start: 0.6300 (mmp) cc_final: 0.5905 (mmp) REVERT: 3 105 ILE cc_start: 0.8629 (mt) cc_final: 0.8406 (mt) REVERT: 3 146 LEU cc_start: 0.8295 (tp) cc_final: 0.8058 (tp) REVERT: 3 202 ILE cc_start: 0.8838 (mt) cc_final: 0.8612 (mt) REVERT: 3 377 ILE cc_start: 0.8087 (mm) cc_final: 0.7780 (mm) REVERT: 3 392 ILE cc_start: 0.8553 (mt) cc_final: 0.8297 (mt) REVERT: 3 489 LYS cc_start: 0.8724 (pttm) cc_final: 0.8317 (pptt) REVERT: 3 491 MET cc_start: 0.6374 (mtt) cc_final: 0.5588 (ppp) REVERT: 4 68 TYR cc_start: 0.8377 (t80) cc_final: 0.8116 (t80) REVERT: 4 70 GLU cc_start: 0.7861 (pt0) cc_final: 0.7312 (pt0) REVERT: 4 113 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7445 (tm-30) REVERT: 4 148 GLU cc_start: 0.8271 (tt0) cc_final: 0.7985 (tm-30) REVERT: 4 152 ASP cc_start: 0.7776 (t0) cc_final: 0.7173 (p0) REVERT: 4 265 ASN cc_start: 0.8574 (m-40) cc_final: 0.8092 (m-40) REVERT: 4 290 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6121 (pt0) REVERT: 4 377 ILE cc_start: 0.8675 (mm) cc_final: 0.8356 (mm) REVERT: 4 421 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7330 (mm-40) REVERT: 5 61 ASP cc_start: 0.7770 (p0) cc_final: 0.7508 (p0) REVERT: 5 100 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7377 (tm-30) REVERT: 5 119 LEU cc_start: 0.8941 (tp) cc_final: 0.8543 (tp) REVERT: 5 148 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7986 (tm-30) REVERT: 5 208 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7461 (ptp90) REVERT: 5 240 THR cc_start: 0.8569 (m) cc_final: 0.8367 (m) REVERT: 5 244 PHE cc_start: 0.8297 (m-10) cc_final: 0.7950 (m-10) REVERT: 5 254 MET cc_start: 0.7050 (pmm) cc_final: 0.6808 (mtt) REVERT: 5 350 GLN cc_start: 0.8059 (tp40) cc_final: 0.7806 (tp-100) REVERT: 5 365 ILE cc_start: 0.8790 (mm) cc_final: 0.8570 (mm) REVERT: 5 478 ASP cc_start: 0.8172 (m-30) cc_final: 0.7950 (m-30) REVERT: 5 489 LYS cc_start: 0.7685 (pttt) cc_final: 0.7063 (tmmt) REVERT: 7 23 LEU cc_start: 0.7575 (tp) cc_final: 0.7351 (tt) REVERT: 7 56 MET cc_start: 0.7513 (tpp) cc_final: 0.7292 (tpp) REVERT: 7 112 TYR cc_start: 0.5409 (t80) cc_final: 0.5149 (t80) REVERT: 7 211 ILE cc_start: 0.5975 (mt) cc_final: 0.3938 (mt) REVERT: 8 28 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8243 (tm-30) REVERT: 8 54 MET cc_start: 0.7854 (mpp) cc_final: 0.7521 (mmp) REVERT: 8 72 MET cc_start: 0.8242 (mtm) cc_final: 0.7720 (tpt) REVERT: 8 97 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7889 (tm-30) REVERT: 8 185 ASN cc_start: 0.8813 (p0) cc_final: 0.8487 (p0) REVERT: 9 154 MET cc_start: 0.8299 (mmp) cc_final: 0.7735 (mmt) REVERT: 9 197 GLU cc_start: 0.8177 (mp0) cc_final: 0.7893 (mp0) REVERT: 9 203 ILE cc_start: 0.8723 (tp) cc_final: 0.8509 (tp) REVERT: 9 206 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8117 (mt0) REVERT: Q 72 MET cc_start: 0.9139 (pmm) cc_final: 0.8880 (pmm) REVERT: Q 125 TYR cc_start: 0.7973 (m-10) cc_final: 0.7722 (m-80) REVERT: Q 132 MET cc_start: 0.7162 (mtt) cc_final: 0.6242 (mtp) REVERT: R 113 ASN cc_start: 0.8606 (m110) cc_final: 0.8350 (m110) REVERT: T 16 LYS cc_start: 0.8072 (mttt) cc_final: 0.6963 (tttp) REVERT: T 34 LYS cc_start: 0.8072 (tppt) cc_final: 0.7267 (mttt) REVERT: V 102 MET cc_start: 0.6154 (ttt) cc_final: 0.5950 (ttp) REVERT: X 31 ASN cc_start: 0.6584 (m110) cc_final: 0.6333 (m-40) REVERT: 6 82 ASP cc_start: 0.5451 (t0) cc_final: 0.4970 (m-30) REVERT: 6 109 MET cc_start: 0.7821 (tmm) cc_final: 0.6557 (mtt) REVERT: 6 152 ASN cc_start: 0.8147 (t0) cc_final: 0.7720 (m110) REVERT: 6 301 ARG cc_start: 0.6494 (ttm170) cc_final: 0.6190 (ttm170) REVERT: 6 302 VAL cc_start: 0.8059 (p) cc_final: 0.7461 (p) REVERT: 6 322 GLN cc_start: 0.2446 (tp-100) cc_final: 0.2120 (pt0) REVERT: 6 338 LEU cc_start: 0.6590 (mt) cc_final: 0.6088 (mt) REVERT: 6 341 HIS cc_start: 0.6675 (p90) cc_final: 0.5419 (m90) REVERT: U 65 MET cc_start: 0.6544 (ppp) cc_final: 0.5473 (mtt) REVERT: U 96 MET cc_start: 0.1581 (ptm) cc_final: 0.0544 (mmt) REVERT: U 140 MET cc_start: 0.8056 (ttt) cc_final: 0.7785 (ptt) REVERT: U 147 LYS cc_start: 0.6367 (mmmm) cc_final: 0.5791 (tptt) REVERT: U 156 MET cc_start: 0.6911 (ptm) cc_final: 0.6576 (ptt) REVERT: U 199 GLN cc_start: 0.6934 (mm110) cc_final: 0.6409 (tm-30) REVERT: U 234 LYS cc_start: 0.6508 (tttt) cc_final: 0.5502 (mptt) REVERT: U 293 LEU cc_start: 0.8140 (mm) cc_final: 0.7802 (mp) REVERT: U 309 MET cc_start: 0.4923 (mtt) cc_final: 0.4387 (mtp) REVERT: U 363 ARG cc_start: 0.6116 (ttt180) cc_final: 0.5732 (mmt-90) REVERT: U 383 LEU cc_start: 0.5959 (mt) cc_final: 0.5408 (tp) REVERT: U 434 LYS cc_start: 0.5544 (pttm) cc_final: 0.5044 (tptt) REVERT: U 460 MET cc_start: 0.6513 (tpp) cc_final: 0.5784 (tpp) REVERT: d 38 GLN cc_start: 0.6648 (mm-40) cc_final: 0.5954 (mt0) REVERT: d 75 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8001 (mmmt) REVERT: d 84 HIS cc_start: 0.7940 (t-90) cc_final: 0.7492 (t-170) REVERT: d 165 GLN cc_start: 0.7125 (tt0) cc_final: 0.5849 (tp40) REVERT: d 186 TYR cc_start: 0.6619 (t80) cc_final: 0.6291 (t80) REVERT: d 189 TYR cc_start: 0.7189 (t80) cc_final: 0.6423 (t80) REVERT: d 346 ASN cc_start: 0.7126 (t0) cc_final: 0.6782 (t0) REVERT: d 349 PRO cc_start: 0.7758 (Cg_endo) cc_final: 0.7447 (Cg_exo) REVERT: a 50 LYS cc_start: 0.8548 (tptm) cc_final: 0.8094 (tptp) REVERT: a 61 MET cc_start: 0.8078 (mtp) cc_final: 0.7525 (mtt) REVERT: a 124 GLU cc_start: 0.6486 (tp30) cc_final: 0.5411 (pp20) REVERT: a 125 LEU cc_start: 0.6385 (mt) cc_final: 0.5928 (mt) REVERT: a 290 LEU cc_start: 0.7883 (mt) cc_final: 0.7438 (tp) REVERT: a 383 ASN cc_start: 0.8849 (t0) cc_final: 0.8541 (m-40) REVERT: a 470 ILE cc_start: 0.6740 (mt) cc_final: 0.6497 (mt) REVERT: a 547 MET cc_start: 0.7927 (ttp) cc_final: 0.7677 (ttp) REVERT: a 565 PHE cc_start: 0.7364 (m-80) cc_final: 0.7088 (m-80) REVERT: a 598 ILE cc_start: 0.7419 (mt) cc_final: 0.7023 (mt) REVERT: a 610 SER cc_start: 0.8049 (t) cc_final: 0.7848 (m) REVERT: a 623 MET cc_start: 0.8485 (ttp) cc_final: 0.8209 (tpp) REVERT: a 624 PHE cc_start: 0.8264 (m-80) cc_final: 0.7945 (m-80) REVERT: a 635 MET cc_start: 0.4508 (mmt) cc_final: 0.4015 (tpt) REVERT: a 740 TYR cc_start: 0.8377 (m-80) cc_final: 0.7769 (m-80) REVERT: a 769 ARG cc_start: 0.5606 (mtm180) cc_final: 0.4698 (mmt180) REVERT: f 29 LEU cc_start: 0.8344 (tp) cc_final: 0.8137 (tp) REVERT: c 317 PHE cc_start: 0.2162 (m-80) cc_final: 0.1941 (m-80) REVERT: c 376 ASN cc_start: 0.7249 (m110) cc_final: 0.6921 (m110) outliers start: 2 outliers final: 0 residues processed: 1830 average time/residue: 0.5825 time to fit residues: 1840.2230 Evaluate side-chains 1585 residues out of total 7059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1585 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 831 random chunks: chunk 523 optimal weight: 7.9990 chunk 702 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 607 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 660 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 678 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 397 ASN ** 0 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 444 HIS 2 207 GLN ** 2 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN 3 262 ASN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 206 GLN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN ** V 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN 6 23 HIS 6 116 GLN 6 296 HIS ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 GLN a 269 ASN ** a 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.168299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139888 restraints weight = 153087.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142526 restraints weight = 96027.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144466 restraints weight = 64174.430| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 66820 Z= 0.270 Angle : 0.694 17.960 90305 Z= 0.360 Chirality : 0.044 0.291 10236 Planarity : 0.005 0.114 11580 Dihedral : 4.759 79.058 9108 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 8319 helix: 1.26 (0.08), residues: 4697 sheet: -0.14 (0.20), residues: 691 loop : -1.62 (0.11), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 2 450 HIS 0.008 0.001 HIS U 443 PHE 0.066 0.002 PHE b 150 TYR 0.051 0.002 TYR o 144 ARG 0.013 0.001 ARG 4 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25214.73 seconds wall clock time: 435 minutes 12.14 seconds (26112.14 seconds total)