Starting phenix.real_space_refine on Fri Jun 28 03:40:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brq_44840/06_2024/9brq_44840.pdb" } resolution = 4.3 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= 0.002 sd= 0.060 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 398 5.16 5 C 43014 2.51 5 N 11353 2.21 5 O 12402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "i PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 139": "OE1" <-> "OE2" Residue "1 GLU 89": "OE1" <-> "OE2" Residue "1 GLU 360": "OE1" <-> "OE2" Residue "3 TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 336": "OE1" <-> "OE2" Residue "4 GLU 490": "OE1" <-> "OE2" Residue "5 TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 336": "OE1" <-> "OE2" Residue "5 GLU 374": "OE1" <-> "OE2" Residue "7 GLU 120": "OE1" <-> "OE2" Residue "7 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 197": "OE1" <-> "OE2" Residue "8 GLU 182": "OE1" <-> "OE2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "6 TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 255": "OE1" <-> "OE2" Residue "U PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 583": "OE1" <-> "OE2" Residue "a GLU 811": "OE1" <-> "OE2" Residue "0 GLU 360": "OE1" <-> "OE2" Residue "0 GLU 606": "OE1" <-> "OE2" Residue "s PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 67167 Number of models: 1 Model: "" Number of chains: 33 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: "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: "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} Chain: "0" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4551 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 3 Chain: "f" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 666 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "s" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1671 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 203} Chain: "e" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Time building chain proxies: 27.17, per 1000 atoms: 0.40 Number of scatterers: 67167 At special positions: 0 Unit cell: (161.15, 216.719, 298.96, 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 398 16.00 O 12402 8.00 N 11353 7.00 C 43014 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: 22.84 Conformation dependent library (CDL) restraints added in 9.1 seconds 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15892 Finding SS restraints... Secondary structure from input PDB file: 299 helices and 45 sheets defined 61.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'b' and resid 7 through 29 removed outlier: 3.802A pdb=" N PHE b 29 " --> pdb=" O CYS b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 43 Processing helix chain 'b' and resid 45 through 81 removed outlier: 3.563A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 87 removed outlier: 3.734A pdb=" N ILE b 86 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'b' and resid 91 through 114 Processing helix chain 'b' and resid 130 through 167 removed outlier: 4.094A pdb=" N GLY b 134 " --> pdb=" O ASN b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 176 removed outlier: 3.648A pdb=" N PHE b 173 " --> pdb=" O PRO b 170 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 177 through 198 removed outlier: 3.717A pdb=" N ILE b 181 " --> pdb=" O LEU b 177 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE b 186 " --> pdb=" O PHE b 182 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 45 removed outlier: 4.294A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET g 23 " --> pdb=" O ALA g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 removed outlier: 3.805A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 80 removed outlier: 4.254A pdb=" N VAL g 60 " --> pdb=" O ILE g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 122 removed outlier: 4.576A pdb=" N PHE g 90 " --> pdb=" O LEU g 86 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA g 122 " --> pdb=" O VAL g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 155 removed outlier: 4.063A pdb=" N MET g 131 " --> pdb=" O LEU g 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE g 132 " --> pdb=" O PHE g 128 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY g 142 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 45 removed outlier: 4.026A pdb=" N PHE h 14 " --> pdb=" O TYR h 10 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 50 No H-bonds generated for 'chain 'h' and resid 48 through 50' Processing helix chain 'h' and resid 51 through 56 Processing helix chain 'h' and resid 56 through 80 removed outlier: 3.795A pdb=" N ILE h 64 " --> pdb=" O VAL h 60 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE h 65 " --> pdb=" O MET h 61 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA h 66 " --> pdb=" O ALA h 62 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 122 removed outlier: 4.251A pdb=" N PHE h 90 " --> pdb=" O LEU h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 127 through 155 removed outlier: 3.710A pdb=" N LYS h 155 " --> pdb=" O ILE h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 12 through 45 removed outlier: 3.559A pdb=" N VAL i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 80 removed outlier: 4.594A pdb=" N ILE i 57 " --> pdb=" O MET i 53 " (cutoff:3.500A) Proline residue: i 58 - end of helix removed outlier: 4.145A pdb=" N ILE i 65 " --> pdb=" O MET i 61 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA i 66 " --> pdb=" O ALA i 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE i 67 " --> pdb=" O GLY i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 121 Processing helix chain 'i' and resid 122 through 123 No H-bonds generated for 'chain 'i' and resid 122 through 123' Processing helix chain 'i' and resid 124 through 126 No H-bonds generated for 'chain 'i' and resid 124 through 126' Processing helix chain 'i' and resid 127 through 155 removed outlier: 3.999A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU i 146 " --> pdb=" O GLY i 142 " (cutoff:3.500A) removed outlier: 3.586A 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 80 removed outlier: 4.019A pdb=" N GLY j 63 " --> pdb=" O VAL j 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL j 72 " --> pdb=" O TYR j 68 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA j 73 " --> pdb=" O GLY j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 removed outlier: 4.159A pdb=" N PHE j 90 " --> pdb=" O LEU j 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA j 116 " --> pdb=" O ILE j 112 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG j 119 " --> pdb=" O ASP j 115 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 154 removed outlier: 4.152A pdb=" N LEU j 141 " --> pdb=" O PHE j 137 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 46 removed outlier: 3.602A pdb=" N VAL k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 50 No H-bonds generated for 'chain 'k' and resid 48 through 50' Processing helix chain 'k' and resid 51 through 56 Processing helix chain 'k' and resid 56 through 63 removed outlier: 3.825A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 63 through 80 Processing helix chain 'k' and resid 86 through 121 removed outlier: 4.121A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (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 155 removed outlier: 4.192A pdb=" N LEU k 141 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 44 removed outlier: 3.949A pdb=" N VAL l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 80 removed outlier: 3.769A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 88 through 120 removed outlier: 3.501A pdb=" N ASP l 115 " --> pdb=" O GLY l 111 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY l 120 " --> pdb=" O ALA l 116 " (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 154 removed outlier: 3.584A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR l 154 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 44 removed outlier: 3.890A pdb=" N VAL m 16 " --> pdb=" O SER m 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 56 removed outlier: 3.644A pdb=" N ILE m 56 " --> pdb=" O ILE m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 58 through 80 Processing helix chain 'm' and resid 86 through 122 removed outlier: 3.850A pdb=" N PHE m 90 " --> pdb=" O LEU m 86 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA m 122 " --> pdb=" O VAL m 118 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 155 Processing helix chain 'n' and resid 11 through 45 Processing helix chain 'n' and resid 48 through 52 removed outlier: 3.502A pdb=" N ILE n 52 " --> pdb=" O PRO n 49 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 55 No H-bonds generated for 'chain 'n' and resid 53 through 55' Processing helix chain 'n' and resid 56 through 62 Processing helix chain 'n' and resid 63 through 80 Processing helix chain 'n' and resid 87 through 124 Processing helix chain 'n' and resid 126 through 155 removed outlier: 4.612A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU n 146 " --> pdb=" O GLY n 142 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE n 147 " --> pdb=" O LEU n 143 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL n 148 " --> pdb=" O TYR n 144 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS n 155 " --> pdb=" O ILE n 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 46 removed outlier: 4.230A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA o 22 " --> pdb=" O GLY o 18 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET o 23 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY o 29 " --> pdb=" O PHE o 25 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 55 removed outlier: 3.525A pdb=" N SER o 55 " --> pdb=" O ILE o 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 52 through 55' Processing helix chain 'o' and resid 56 through 79 Processing helix chain 'o' and resid 88 through 124 removed outlier: 3.515A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN o 123 " --> pdb=" O ARG o 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 126 through 155 removed outlier: 4.346A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL o 148 " --> pdb=" O TYR o 144 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA o 149 " --> pdb=" O GLY o 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS o 155 " --> pdb=" O ILE o 151 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 256 through 266 Processing helix chain '1' and resid 280 through 294 removed outlier: 4.149A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Proline residue: 1 292 - end of helix Processing helix chain '1' and resid 321 through 340 removed outlier: 3.868A pdb=" N ALA 1 325 " --> pdb=" O ALA 1 321 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 366 removed outlier: 3.888A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 388 removed outlier: 3.576A pdb=" N ARG 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 419 through 429 Processing helix chain '1' and resid 436 through 442 Processing helix chain '1' and resid 457 through 469 removed outlier: 4.275A pdb=" N GLU 1 463 " --> pdb=" O ARG 1 459 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 497 removed outlier: 4.584A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.140A 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: 3.719A pdb=" N ARG 1 530 " --> pdb=" O PRO 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 574 through 584 Processing helix chain '1' 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: 3.826A pdb=" N SER 2 262 " --> pdb=" O VAL 2 258 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 294 Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 304 through 308 removed outlier: 3.984A pdb=" N ARG 2 308 " --> pdb=" O SER 2 304 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 304 through 308' Processing helix chain '2' and resid 319 through 340 removed outlier: 4.225A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET 2 340 " --> pdb=" O TYR 2 336 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 366 Processing helix chain '2' and resid 377 through 388 removed outlier: 3.926A 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 436 through 442 Processing helix chain '2' and resid 461 through 469 Processing helix chain '2' and resid 471 through 497 removed outlier: 3.605A pdb=" N LEU 2 475 " --> pdb=" O GLU 2 471 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE 2 492 " --> pdb=" O ASP 2 488 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY 2 497 " --> pdb=" O VAL 2 493 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 518 Processing helix chain '2' and resid 526 through 530 removed outlier: 3.585A pdb=" N ARG 2 530 " --> pdb=" O PRO 2 527 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 560 removed outlier: 4.465A 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 removed outlier: 3.729A pdb=" N GLU 2 616 " --> pdb=" O PHE 2 612 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 128 removed outlier: 3.895A pdb=" N LEU 3 128 " --> pdb=" O GLU 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 209 Processing helix chain '3' and resid 237 through 252 removed outlier: 3.732A pdb=" N ALA 3 241 " --> pdb=" O ASN 3 237 " (cutoff:3.500A) removed outlier: 3.555A 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 267 through 272 removed outlier: 3.922A pdb=" N GLU 3 270 " --> pdb=" O PRO 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 288 Processing helix chain '3' and resid 299 through 314 removed outlier: 3.865A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (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: 3.545A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 401 through 406 removed outlier: 3.792A pdb=" N ILE 3 406 " --> pdb=" O MET 3 402 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 440 removed outlier: 4.024A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY 3 440 " --> pdb=" O LYS 3 436 " (cutoff:3.500A) Processing helix chain '3' and resid 441 through 444 Processing helix chain '3' and resid 445 through 462 Processing helix chain '3' and resid 472 through 485 Processing helix chain '3' and resid 486 through 487 No H-bonds generated for 'chain '3' and resid 486 through 487' Processing helix chain '3' and resid 488 through 492 removed outlier: 3.752A pdb=" N MET 3 491 " --> pdb=" O PRO 3 488 " (cutoff:3.500A) Processing helix chain '3' and resid 496 through 504 Processing helix chain '4' and resid 124 through 128 removed outlier: 3.515A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 198 through 209 removed outlier: 3.814A pdb=" N ILE 4 202 " --> pdb=" O PRO 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 224 removed outlier: 3.547A pdb=" N TYR 4 222 " --> pdb=" O ASP 4 218 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU 4 224 " --> pdb=" O VAL 4 220 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 252 Processing helix chain '4' and resid 253 through 255 No H-bonds generated for 'chain '4' and resid 253 through 255' Processing helix chain '4' and resid 268 through 272 Processing helix chain '4' and resid 273 through 288 removed outlier: 3.633A pdb=" N ALA 4 278 " --> pdb=" O THR 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 315 removed outlier: 3.671A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 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: 3.682A pdb=" N ARG 4 386 " --> pdb=" O GLN 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 399 through 403 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 486 removed outlier: 4.081A pdb=" N ILE 4 486 " --> pdb=" O GLN 4 482 " (cutoff:3.500A) Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 174 through 182 removed outlier: 3.630A pdb=" N MET 5 180 " --> pdb=" O ALA 5 176 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER 5 182 " --> pdb=" O ASP 5 178 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 219 through 224 Processing helix chain '5' and resid 237 through 252 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 removed outlier: 3.656A pdb=" N ARG 5 271 " --> pdb=" O PRO 5 267 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE 5 272 " --> pdb=" O THR 5 268 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 267 through 272' Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 315 removed outlier: 3.519A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 326 through 336 removed outlier: 3.622A pdb=" N ASP 5 330 " --> pdb=" O TYR 5 326 " (cutoff:3.500A) 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 Processing helix chain '5' and resid 401 through 406 Processing helix chain '5' and resid 414 through 440 removed outlier: 3.956A pdb=" N VAL 5 438 " --> pdb=" O ALA 5 434 " (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 501 Processing helix chain '7' and resid 12 through 77 removed outlier: 3.750A pdb=" N GLU 7 60 " --> pdb=" O MET 7 56 " (cutoff:3.500A) Processing helix chain '7' and resid 79 through 86 removed outlier: 3.565A pdb=" N VAL 7 83 " --> pdb=" O PHE 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 214 removed outlier: 4.201A pdb=" N ILE 7 177 " --> pdb=" O GLU 7 173 " (cutoff:3.500A) Proline residue: 7 178 - end of helix Processing helix chain '8' and resid 3 through 106 Processing helix chain '8' and resid 108 through 128 removed outlier: 3.542A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 8 128 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 160 Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 195 through 216 Proline residue: 8 209 - end of helix Processing helix chain '9' and resid 4 through 107 removed outlier: 3.846A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 4.404A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 140 through 160 Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 217 Proline residue: 9 209 - end of helix Processing helix chain 'Q' and resid 3 through 107 removed outlier: 3.872A pdb=" N ASP Q 7 " --> pdb=" O LEU Q 3 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL Q 46 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 128 removed outlier: 3.631A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 160 Proline residue: Q 153 - end of helix removed outlier: 3.682A pdb=" N LYS Q 156 " --> pdb=" O ILE Q 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 217 removed outlier: 3.759A pdb=" N VAL Q 211 " --> pdb=" O MET Q 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 105 removed outlier: 4.730A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 removed outlier: 4.019A pdb=" N ASN T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 93 through 104 Processing helix chain 'V' and resid 5 through 105 removed outlier: 3.708A pdb=" N ASN V 91 " --> pdb=" O SER V 87 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU V 93 " --> pdb=" O GLN V 89 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) removed outlier: 3.651A 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 74 through 81 Processing helix chain 'X' and resid 103 through 109 Processing helix chain '6' and resid 15 through 22 removed outlier: 4.011A pdb=" N TRP 6 19 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) Processing helix chain '6' and resid 50 through 80 removed outlier: 4.133A pdb=" N LEU 6 80 " --> pdb=" O MET 6 76 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 117 through 157 Processing helix chain '6' and resid 190 through 192 No H-bonds generated for 'chain '6' and resid 190 through 192' Processing helix chain '6' and resid 193 through 205 removed outlier: 6.192A pdb=" N GLU 6 202 " --> pdb=" O ILE 6 198 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR 6 203 " --> pdb=" O LYS 6 199 " (cutoff:3.500A) Processing helix chain '6' and resid 231 through 243 removed outlier: 4.441A pdb=" N GLU 6 243 " --> pdb=" O HIS 6 239 " (cutoff:3.500A) Processing helix chain '6' and resid 254 through 311 removed outlier: 3.797A pdb=" N MET 6 258 " --> pdb=" O ASN 6 254 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP 6 261 " --> pdb=" O GLU 6 257 " (cutoff:3.500A) Proline residue: 6 278 - end of helix Processing helix chain '6' and resid 327 through 344 removed outlier: 4.495A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU 6 342 " --> pdb=" O LEU 6 338 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP 6 343 " --> pdb=" O TYR 6 339 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 45 through 52 Processing helix chain 'U' and resid 58 through 65 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 86 through 98 removed outlier: 4.388A pdb=" N TYR U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 104 Processing helix chain 'U' and resid 123 through 127 removed outlier: 3.707A pdb=" N PHE U 126 " --> pdb=" O TRP U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 Processing helix chain 'U' and resid 158 through 163 removed outlier: 3.599A pdb=" N TYR U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 169 removed outlier: 3.778A pdb=" N ILE U 168 " --> pdb=" O TYR U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 220 removed outlier: 3.716A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (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 261 Processing helix chain 'U' and resid 264 through 276 removed outlier: 3.554A pdb=" N VAL U 268 " --> pdb=" O ASN U 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 295 Processing helix chain 'U' and resid 303 through 312 removed outlier: 4.540A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 314 through 323 removed outlier: 3.528A pdb=" N GLN U 323 " --> pdb=" O GLU U 319 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 350 removed outlier: 3.842A 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 379 Processing helix chain 'U' and resid 380 through 382 No H-bonds generated for 'chain 'U' and resid 380 through 382' Processing helix chain 'U' and resid 385 through 387 No H-bonds generated for 'chain 'U' and resid 385 through 387' Processing helix chain 'U' and resid 388 through 401 removed outlier: 3.618A pdb=" N GLU U 399 " --> pdb=" O THR U 395 " (cutoff:3.500A) Processing helix chain 'U' and resid 403 through 420 Processing helix chain 'U' and resid 421 through 432 Processing helix chain 'U' and resid 432 through 441 removed outlier: 3.511A pdb=" N LEU U 436 " --> pdb=" O GLY U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 445 through 460 Processing helix chain 'd' and resid 8 through 26 removed outlier: 6.985A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY d 26 " --> pdb=" O GLY d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 37 Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 66 through 87 removed outlier: 3.754A pdb=" N ILE d 70 " --> pdb=" O THR d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 113 removed outlier: 3.840A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 115 through 119 Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.930A pdb=" N LEU d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) 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: 4.283A pdb=" N ASP d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE d 168 " --> pdb=" O PHE d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 176 Processing helix chain 'd' and resid 177 through 200 removed outlier: 3.561A pdb=" N ILE d 181 " --> pdb=" O ASN d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 Processing helix chain 'd' and resid 289 through 308 removed outlier: 3.796A pdb=" N ASN d 308 " --> pdb=" O LEU d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 339 Processing helix chain 'a' and resid 19 through 33 removed outlier: 4.597A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 50 removed outlier: 3.910A pdb=" N LYS a 50 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 92 through 134 removed outlier: 4.161A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU a 124 " --> pdb=" O ARG a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 198 removed outlier: 4.523A pdb=" N ARG a 192 " --> pdb=" O PRO a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 248 Processing helix chain 'a' and resid 258 through 316 removed outlier: 3.982A pdb=" N LYS a 262 " --> pdb=" O PRO a 258 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG a 298 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL a 299 " --> pdb=" O LYS a 295 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP a 300 " --> pdb=" O ASN a 296 " (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: 4.256A 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 433 removed outlier: 3.654A pdb=" N ARG a 433 " --> pdb=" O TRP a 429 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 440 Processing helix chain 'a' and resid 444 through 453 removed outlier: 3.705A pdb=" N GLY a 453 " --> pdb=" O MET a 449 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 472 Processing helix chain 'a' and resid 527 through 533 removed outlier: 4.039A pdb=" N ASN a 531 " --> pdb=" O ASP a 527 " (cutoff:3.500A) Processing helix chain 'a' and resid 535 through 571 removed outlier: 4.248A pdb=" N PHE a 539 " --> pdb=" O ASN a 535 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER a 542 " --> pdb=" O THR a 538 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE a 543 " --> pdb=" O PHE a 539 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS a 544 " --> pdb=" O LEU a 540 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER a 563 " --> pdb=" O GLY a 559 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU a 564 " --> pdb=" O VAL a 560 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 4.452A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 605 removed outlier: 3.756A pdb=" N LEU a 590 " --> pdb=" O PHE a 586 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR a 605 " --> pdb=" O LYS a 601 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 613 removed outlier: 5.433A pdb=" N ARG a 611 " --> pdb=" O HIS a 608 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN a 612 " --> pdb=" O SER a 609 " (cutoff:3.500A) Processing helix chain 'a' and resid 617 through 626 removed outlier: 3.575A pdb=" N ILE a 621 " --> pdb=" O LEU a 617 " (cutoff:3.500A) Processing helix chain 'a' and resid 639 through 654 removed outlier: 3.584A pdb=" N ILE a 643 " --> pdb=" O GLY a 639 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS a 654 " --> pdb=" O VAL a 650 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 674 Processing helix chain 'a' and resid 716 through 740 Processing helix chain 'a' and resid 740 through 762 removed outlier: 4.535A pdb=" N TRP a 744 " --> pdb=" O TYR a 740 " (cutoff:3.500A) Processing helix chain 'a' and resid 769 through 791 removed outlier: 4.098A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU a 777 " --> pdb=" O GLY a 773 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE a 778 " --> pdb=" O GLY a 774 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) Processing helix chain 'a' and resid 794 through 811 Processing helix chain 'c' and resid 416 through 442 removed outlier: 3.544A pdb=" N SER c 442 " --> pdb=" O HIS c 438 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 328 Processing helix chain '0' and resid 105 through 114 removed outlier: 4.108A pdb=" N SER 0 111 " --> pdb=" O SER 0 107 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 0 113 " --> pdb=" O ILE 0 109 " (cutoff:3.500A) Processing helix chain '0' and resid 233 through 238 Processing helix chain '0' and resid 257 through 267 removed outlier: 3.926A pdb=" N GLN 0 261 " --> pdb=" O THR 0 257 " (cutoff:3.500A) Processing helix chain '0' and resid 281 through 291 Processing helix chain '0' and resid 319 through 339 removed outlier: 3.613A pdb=" N ARG 0 323 " --> pdb=" O PRO 0 319 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 352 through 366 Processing helix chain '0' and resid 376 through 388 removed outlier: 4.508A pdb=" N ALA 0 380 " --> pdb=" O ALA 0 376 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG 0 388 " --> pdb=" O SER 0 384 " (cutoff:3.500A) Processing helix chain '0' and resid 419 through 429 Processing helix chain '0' and resid 436 through 441 Processing helix chain '0' and resid 461 through 468 Processing helix chain '0' and resid 471 through 494 removed outlier: 4.057A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR 0 477 " --> pdb=" O VAL 0 473 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 520 removed outlier: 3.726A pdb=" N LYS 0 506 " --> pdb=" O ALA 0 502 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR 0 508 " --> pdb=" O THR 0 504 " (cutoff:3.500A) Processing helix chain '0' and resid 526 through 530 Processing helix chain '0' and resid 533 through 537 Processing helix chain '0' and resid 538 through 552 Processing helix chain '0' and resid 566 through 575 removed outlier: 3.788A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 0 575 " --> pdb=" O ARG 0 571 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 584 removed outlier: 4.035A pdb=" N TYR 0 579 " --> pdb=" O GLY 0 575 " (cutoff:3.500A) 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 588 through 593 removed outlier: 3.725A pdb=" N GLY 0 593 " --> pdb=" O PRO 0 589 " (cutoff:3.500A) Processing helix chain '0' and resid 593 through 614 Processing helix chain 'f' and resid 8 through 11 Processing helix chain 'f' and resid 12 through 36 Processing helix chain 'f' and resid 55 through 89 removed outlier: 3.709A pdb=" N CYS f 69 " --> pdb=" O VAL f 65 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE f 71 " --> pdb=" O TYR f 67 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) Processing helix chain 's' and resid 19 through 24 Processing helix chain 's' and resid 24 through 45 removed outlier: 3.981A pdb=" N PHE s 28 " --> pdb=" O GLU s 24 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA s 42 " --> pdb=" O ILE s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 79 Processing helix chain 's' and resid 101 through 129 Processing helix chain 's' and resid 129 through 134 Processing helix chain 's' and resid 138 through 170 Processing helix chain 's' and resid 173 through 181 removed outlier: 4.055A pdb=" N ILE s 177 " --> pdb=" O ASP s 173 " (cutoff:3.500A) Processing helix chain 's' and resid 199 through 227 Processing helix chain 'e' and resid 6 through 28 Proline residue: e 25 - end of helix removed outlier: 4.080A pdb=" N VAL e 28 " --> pdb=" O GLY e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 70 through 79 Processing sheet with id=AA1, first strand: chain '1' and resid 18 through 25 removed outlier: 5.604A pdb=" N VAL 1 21 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS 1 32 " --> pdb=" O VAL 1 21 " (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: 6.805A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 7.103A 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 '2' and resid 50 through 58 removed outlier: 6.903A pdb=" N THR 2 63 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU 2 57 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N MET 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 61 through 66 current: chain '3' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 61 current: chain '3' and resid 81 through 90 removed outlier: 6.942A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.054A 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: 5.887A pdb=" N VAL 4 86 " --> pdb=" O GLN 4 97 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN 4 97 " --> pdb=" O VAL 4 86 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU 4 88 " --> pdb=" O VAL 4 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '8' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 164 through 167 current: chain '8' and resid 190 through 192 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 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 98 through 99 current: chain '1' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 309 through 312 current: chain '1' and resid 401 through 408 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '1' and resid 133 through 135 removed outlier: 3.613A 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: 7.219A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 152 through 156 removed outlier: 7.161A pdb=" N ILE 1 166 " --> pdb=" O TYR 1 153 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE 1 155 " --> pdb=" O HIS 1 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS 1 164 " --> pdb=" O ILE 1 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 295 through 296 Processing sheet with id=AA8, first strand: chain '2' and resid 87 through 90 Processing sheet with id=AA9, 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 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 309 through 312 current: chain '2' and resid 402 through 410 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '2' and resid 164 through 167 removed outlier: 7.080A pdb=" N HIS 2 164 " --> pdb=" O ILE 2 155 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE 2 155 " --> pdb=" O HIS 2 164 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE 2 166 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 146 through 147 removed outlier: 6.710A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE 2 179 " --> pdb=" O VAL 2 191 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL 2 191 " --> pdb=" O ILE 2 179 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE 2 203 " --> pdb=" O VAL 2 191 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU 2 193 " --> pdb=" O GLU 2 201 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU 2 201 " --> pdb=" O GLU 2 193 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU 2 195 " --> pdb=" O VAL 2 199 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL 2 199 " --> pdb=" O GLU 2 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 120 through 123 removed outlier: 3.766A pdb=" N ASP 3 149 " --> pdb=" O VAL 3 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 131 through 132 removed outlier: 3.589A pdb=" N PHE 3 132 " --> pdb=" O LEU 3 259 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE 3 229 " --> pdb=" O CYS 3 258 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE 3 260 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE 3 231 " --> pdb=" O PHE 3 260 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA 3 232 " --> pdb=" O ILE 3 296 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL 3 293 " --> pdb=" O THR 3 349 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE 3 351 " --> pdb=" O VAL 3 293 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL 3 295 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 170 through 171 Processing sheet with id=AB6, first strand: chain '3' and resid 192 through 193 Processing sheet with id=AB7, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AB8, first strand: chain '4' and resid 131 through 132 removed outlier: 3.779A pdb=" N THR 4 298 " --> pdb=" O ALA 4 232 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR 4 349 " --> pdb=" O VAL 4 293 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU 4 297 " --> pdb=" O ILE 4 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 163 through 164 removed outlier: 4.654A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 170 through 171 removed outlier: 3.596A pdb=" N GLY 4 211 " --> pdb=" O GLN 4 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '5' and resid 59 through 60 removed outlier: 6.838A pdb=" N LYS 5 93 " --> pdb=" O VAL 5 89 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL 5 89 " --> pdb=" O LYS 5 93 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL 5 95 " --> pdb=" O LEU 5 87 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU 5 70 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE 5 71 " --> pdb=" O THR 5 115 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU 5 45 " --> pdb=" O PHE 5 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AC4, first strand: chain '5' and resid 131 through 132 removed outlier: 6.212A pdb=" N PHE 5 132 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU 5 263 " --> pdb=" O PHE 5 132 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N CYS 5 258 " --> pdb=" O PHE 5 227 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE 5 229 " --> pdb=" O CYS 5 258 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE 5 260 " --> pdb=" O ILE 5 229 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE 5 231 " --> pdb=" O PHE 5 260 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASN 5 262 " --> pdb=" O PHE 5 231 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA 5 233 " --> pdb=" O ASN 5 262 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA 5 228 " --> pdb=" O LEU 5 294 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE 5 296 " --> pdb=" O ALA 5 228 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL 5 230 " --> pdb=" O ILE 5 296 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE 5 191 " --> pdb=" O LEU 5 354 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET 5 356 " --> pdb=" O ILE 5 191 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER 5 193 " --> pdb=" O MET 5 356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 376 through 379 removed outlier: 6.021A pdb=" N TYR 5 378 " --> pdb=" O PRO 5 396 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 92 through 101 Processing sheet with id=AC7, first strand: chain '9' and resid 164 through 167 removed outlier: 3.645A pdb=" N ILE 9 183 " --> pdb=" O VAL 9 192 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL 9 192 " --> pdb=" O ILE 9 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 36 through 38 removed outlier: 3.870A pdb=" N LEU X 37 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY X 12 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN X 67 " --> pdb=" O ILE X 11 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE X 64 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE X 91 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE X 66 " --> pdb=" O ILE X 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 34 through 37 removed outlier: 3.734A pdb=" N ILE 6 374 " --> pdb=" O PHE 6 4 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 92 through 93 removed outlier: 4.052A pdb=" N VAL 6 96 " --> pdb=" O ALA 6 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 182 through 185 removed outlier: 7.060A pdb=" N LEU 6 224 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN 6 214 " --> pdb=" O ASN 6 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 325 through 333 Processing sheet with id=AD4, first strand: chain 'a' and resid 205 through 214 removed outlier: 3.615A pdb=" N ARG a 205 " --> pdb=" O ILE a 228 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN a 211 " --> pdb=" O VAL a 222 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL a 222 " --> pdb=" O ASN a 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 507 through 509 removed outlier: 3.567A pdb=" N LEU a 508 " --> pdb=" O LEU e 68 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU e 68 " --> pdb=" O LEU a 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'c' and resid 252 through 253 removed outlier: 4.458A pdb=" N VAL c 252 " --> pdb=" O PHE c 263 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE c 263 " --> pdb=" O VAL c 252 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER c 362 " --> pdb=" O SER c 409 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 267 through 271 removed outlier: 3.710A pdb=" N ASN c 267 " --> pdb=" O HIS c 391 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN c 387 " --> pdb=" O ALA c 271 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 295 through 297 removed outlier: 4.939A pdb=" N VAL c 315 " --> pdb=" O TYR c 307 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA c 313 " --> pdb=" O PRO c 309 " (cutoff:3.500A) removed outlier: 4.116A 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 336 current: chain 'c' and resid 346 through 350 Processing sheet with id=AD9, first strand: chain '0' and resid 18 through 22 removed outlier: 4.059A pdb=" N THR 0 30 " --> pdb=" O HIS 0 22 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG 0 44 " --> pdb=" O LEU 0 80 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AE2, first strand: chain '0' and resid 98 through 99 removed outlier: 6.671A pdb=" N ILE 0 272 " --> pdb=" O ALA 0 310 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL 0 312 " --> pdb=" O ILE 0 272 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR 0 274 " --> pdb=" O VAL 0 312 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL 0 271 " --> pdb=" O HIS 0 343 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL 0 344 " --> pdb=" O SER 0 405 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL 0 407 " --> pdb=" O VAL 0 344 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET 0 346 " --> pdb=" O VAL 0 407 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '0' and resid 165 through 167 removed outlier: 7.437A pdb=" N ILE 0 166 " --> pdb=" O TYR 0 153 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU 0 134 " --> pdb=" O ASN 0 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0' and resid 176 through 179 removed outlier: 5.450A pdb=" N VAL 0 176 " --> pdb=" O GLU 0 195 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU 0 195 " --> pdb=" O VAL 0 176 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR 0 178 " --> pdb=" O GLU 0 193 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU 0 192 " --> pdb=" O PHE 0 203 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '0' and resid 219 through 220 removed outlier: 3.777A pdb=" N GLU 0 219 " --> pdb=" O LYS 0 393 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '0' and resid 246 through 247 Processing sheet with id=AE7, first strand: chain '0' and resid 296 through 298 Processing sheet with id=AE8, first strand: chain 's' and resid 67 through 72 removed outlier: 6.451A pdb=" N SER s 54 " --> pdb=" O GLU s 193 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU s 193 " --> pdb=" O SER s 54 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU s 56 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N CYS s 191 " --> pdb=" O GLU s 56 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 's' and resid 81 through 85 4082 hydrogen bonds defined for protein. 11994 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: 26.84 Time building geometry restraints manager: 25.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 11135 1.31 - 1.44: 17441 1.44 - 1.57: 39153 1.57 - 1.69: 2 1.69 - 1.82: 703 Bond restraints: 68434 Sorted by residual: bond pdb=" C TYR j 87 " pdb=" O TYR j 87 " ideal model delta sigma weight residual 1.236 1.317 -0.081 1.17e-02 7.31e+03 4.82e+01 bond pdb=" C MET j 61 " pdb=" O MET j 61 " ideal model delta sigma weight residual 1.236 1.322 -0.086 1.26e-02 6.30e+03 4.62e+01 bond pdb=" C ILE o 134 " pdb=" O ILE o 134 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.13e-02 7.83e+03 2.62e+01 bond pdb=" C ILE o 147 " pdb=" O ILE o 147 " ideal model delta sigma weight residual 1.237 1.184 0.052 1.14e-02 7.69e+03 2.11e+01 bond pdb=" C ALA o 138 " pdb=" O ALA o 138 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.15e-02 7.56e+03 1.70e+01 ... (remaining 68429 not shown) Histogram of bond angle deviations from ideal: 95.26 - 103.05: 444 103.05 - 110.83: 21589 110.83 - 118.62: 32422 118.62 - 126.41: 37298 126.41 - 134.19: 740 Bond angle restraints: 92493 Sorted by residual: angle pdb=" N SER l 102 " pdb=" CA SER l 102 " pdb=" C SER l 102 " ideal model delta sigma weight residual 111.71 103.13 8.58 1.15e+00 7.56e-01 5.56e+01 angle pdb=" N TYR o 144 " pdb=" CA TYR o 144 " pdb=" C TYR o 144 " ideal model delta sigma weight residual 111.07 103.50 7.57 1.07e+00 8.73e-01 5.01e+01 angle pdb=" N LEU j 104 " pdb=" CA LEU j 104 " pdb=" C LEU j 104 " ideal model delta sigma weight residual 111.28 103.76 7.52 1.09e+00 8.42e-01 4.76e+01 angle pdb=" CA TYR j 87 " pdb=" C TYR j 87 " pdb=" O TYR j 87 " ideal model delta sigma weight residual 120.80 127.04 -6.24 1.05e+00 9.07e-01 3.53e+01 angle pdb=" N GLU T 52 " pdb=" CA GLU T 52 " pdb=" CB GLU T 52 " ideal model delta sigma weight residual 110.16 118.65 -8.49 1.48e+00 4.57e-01 3.29e+01 ... (remaining 92488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 37545 17.95 - 35.89: 3068 35.89 - 53.84: 540 53.84 - 71.78: 98 71.78 - 89.73: 56 Dihedral angle restraints: 41307 sinusoidal: 16548 harmonic: 24759 Sorted by residual: dihedral pdb=" CA GLU 0 387 " pdb=" C GLU 0 387 " pdb=" N ARG 0 388 " pdb=" CA ARG 0 388 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU 3 146 " pdb=" C LEU 3 146 " pdb=" N ALA 3 147 " pdb=" CA ALA 3 147 " ideal model delta harmonic sigma weight residual 180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA TYR 0 386 " pdb=" C TYR 0 386 " pdb=" N GLU 0 387 " pdb=" CA GLU 0 387 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 41304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 8544 0.058 - 0.116: 1655 0.116 - 0.173: 260 0.173 - 0.231: 21 0.231 - 0.289: 3 Chirality restraints: 10483 Sorted by residual: chirality pdb=" CG LEU U 101 " pdb=" CB LEU U 101 " pdb=" CD1 LEU U 101 " pdb=" CD2 LEU U 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB THR e 15 " pdb=" CA THR e 15 " pdb=" OG1 THR e 15 " pdb=" CG2 THR e 15 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE j 67 " pdb=" N ILE j 67 " pdb=" C ILE j 67 " pdb=" CB ILE j 67 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 10480 not shown) Planarity restraints: 11849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL j 60 " 0.027 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C VAL j 60 " -0.089 2.00e-02 2.50e+03 pdb=" O VAL j 60 " 0.033 2.00e-02 2.50e+03 pdb=" N MET j 61 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 135 " 0.028 2.00e-02 2.50e+03 2.92e-02 1.70e+01 pdb=" CG TYR b 135 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR b 135 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR b 135 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR b 135 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR b 135 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR b 135 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR b 135 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU o 133 " 0.021 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C LEU o 133 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU o 133 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE o 134 " 0.023 2.00e-02 2.50e+03 ... (remaining 11846 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 22266 2.85 - 3.36: 75196 3.36 - 3.88: 111906 3.88 - 4.39: 127234 4.39 - 4.90: 202725 Nonbonded interactions: 539327 Sorted by model distance: nonbonded pdb=" O LEU b 41 " pdb=" OG1 THR b 44 " model vdw 2.339 2.440 nonbonded pdb=" O GLN V 41 " pdb=" OE1 GLU V 45 " model vdw 2.389 3.040 nonbonded pdb=" O LEU 2 605 " pdb=" OE1 GLN 2 609 " model vdw 2.394 3.040 nonbonded pdb=" O ARG T 48 " pdb=" OE1 GLU T 52 " model vdw 2.395 3.040 nonbonded pdb=" O ALA 8 32 " pdb=" OE1 GLU 8 36 " model vdw 2.403 3.040 ... (remaining 539322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = (chain '1' and (resid 17 through 251 or resid 256 through 495 or resid 501 throu \ gh 559 or resid 565 through 615)) selection = (chain '2' and (resid 17 through 251 or resid 256 through 495 or resid 501 throu \ gh 559 or resid 565 through 615)) } 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: 6.010 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: 0.070 Extract box with map and model: 18.570 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 144.170 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.460 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.004 0.086 68434 Z= 0.294 Angle : 0.830 10.645 92493 Z= 0.469 Chirality : 0.047 0.289 10483 Planarity : 0.006 0.096 11849 Dihedral : 13.739 89.729 25415 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 0.15 % Allowed : 0.37 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: -0.58 (0.09), residues: 8508 helix: 0.58 (0.07), residues: 4781 sheet: -1.68 (0.19), residues: 697 loop : -1.54 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP s 154 HIS 0.009 0.001 HIS s 78 PHE 0.040 0.002 PHE Q 18 TYR 0.070 0.002 TYR b 135 ARG 0.018 0.001 ARG 0 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1156 time to evaluate : 6.002 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 19 MET cc_start: 0.9365 (tmm) cc_final: 0.8837 (ptp) REVERT: b 56 LEU cc_start: 0.9576 (mt) cc_final: 0.9271 (pp) REVERT: b 69 ILE cc_start: 0.9425 (mt) cc_final: 0.9211 (mt) REVERT: b 107 MET cc_start: 0.8949 (mmp) cc_final: 0.8635 (mmm) REVERT: b 178 ILE cc_start: 0.9047 (pt) cc_final: 0.8808 (pt) REVERT: b 203 MET cc_start: 0.7431 (tmm) cc_final: 0.7154 (ppp) REVERT: g 36 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8866 (mmmm) REVERT: g 37 SER cc_start: 0.9315 (m) cc_final: 0.8964 (p) REVERT: g 47 MET cc_start: 0.9273 (mmm) cc_final: 0.8979 (mmp) REVERT: g 53 MET cc_start: 0.8571 (mmp) cc_final: 0.8247 (mmp) REVERT: g 115 ASP cc_start: 0.7617 (t70) cc_final: 0.6487 (t0) REVERT: g 123 GLN cc_start: 0.8764 (mp10) cc_final: 0.8482 (mp10) REVERT: g 127 LEU cc_start: 0.9258 (mt) cc_final: 0.8690 (pp) REVERT: h 23 MET cc_start: 0.8842 (tpt) cc_final: 0.8360 (mtt) REVERT: h 32 TYR cc_start: 0.6960 (m-80) cc_final: 0.6440 (m-80) REVERT: h 41 ILE cc_start: 0.9025 (mt) cc_final: 0.8708 (mm) REVERT: h 53 MET cc_start: 0.7012 (ttt) cc_final: 0.6615 (tmm) REVERT: h 54 LYS cc_start: 0.9476 (ptmt) cc_final: 0.9276 (ptmt) REVERT: h 76 ILE cc_start: 0.9090 (mt) cc_final: 0.8861 (tt) REVERT: h 137 PHE cc_start: 0.8955 (t80) cc_final: 0.8753 (t80) REVERT: j 25 PHE cc_start: 0.8937 (m-10) cc_final: 0.8482 (m-10) REVERT: j 61 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6229 (tmm) REVERT: j 140 VAL cc_start: 0.9493 (p) cc_final: 0.9153 (m) REVERT: j 155 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.5998 (tppt) REVERT: k 53 MET cc_start: 0.6315 (ttt) cc_final: 0.6015 (ttt) REVERT: k 74 VAL cc_start: 0.8645 (m) cc_final: 0.8430 (p) REVERT: k 131 MET cc_start: 0.8943 (ttp) cc_final: 0.8391 (ttt) REVERT: l 53 MET cc_start: 0.5735 (tmm) cc_final: 0.4812 (tpt) REVERT: l 147 ILE cc_start: 0.8638 (mm) cc_final: 0.8319 (mm) REVERT: n 25 PHE cc_start: 0.9466 (m-80) cc_final: 0.9157 (m-10) REVERT: n 54 LYS cc_start: 0.9591 (mmmt) cc_final: 0.9236 (tttt) REVERT: n 61 MET cc_start: 0.8908 (ttm) cc_final: 0.8313 (ppp) REVERT: n 78 ASN cc_start: 0.7588 (m-40) cc_final: 0.7175 (p0) REVERT: n 135 LEU cc_start: 0.8108 (tp) cc_final: 0.7778 (tt) REVERT: o 136 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8999 (mt) REVERT: o 146 LEU cc_start: 0.9017 (tp) cc_final: 0.7553 (tp) REVERT: 1 95 MET cc_start: 0.9208 (tpp) cc_final: 0.8925 (tpp) REVERT: 1 229 THR cc_start: 0.8724 (m) cc_final: 0.8482 (p) REVERT: 1 277 CYS cc_start: 0.8502 (t) cc_final: 0.7891 (t) REVERT: 1 318 MET cc_start: 0.9480 (mmp) cc_final: 0.9246 (mmp) REVERT: 1 340 MET cc_start: 0.9054 (ttt) cc_final: 0.8672 (tpp) REVERT: 1 385 PHE cc_start: 0.9420 (t80) cc_final: 0.9211 (t80) REVERT: 1 461 LEU cc_start: 0.9455 (mt) cc_final: 0.9012 (pp) REVERT: 1 540 MET cc_start: 0.9223 (mtp) cc_final: 0.8875 (mtp) REVERT: 2 95 MET cc_start: 0.8084 (tpp) cc_final: 0.7775 (tpp) REVERT: 2 318 MET cc_start: 0.9631 (mmp) cc_final: 0.9257 (mmm) REVERT: 2 487 GLU cc_start: 0.9562 (tp30) cc_final: 0.9270 (tm-30) REVERT: 2 544 MET cc_start: 0.9693 (mtp) cc_final: 0.9358 (mmt) REVERT: 2 550 MET cc_start: 0.9685 (tpt) cc_final: 0.9263 (tpp) REVERT: 2 574 MET cc_start: 0.8134 (mpp) cc_final: 0.7801 (mpp) REVERT: 2 584 MET cc_start: 0.8667 (ppp) cc_final: 0.8348 (ppp) REVERT: 3 127 MET cc_start: 0.9431 (ttp) cc_final: 0.9199 (ttm) REVERT: 3 154 MET cc_start: 0.8986 (tpp) cc_final: 0.8742 (mmm) REVERT: 3 238 MET cc_start: 0.9275 (ppp) cc_final: 0.8912 (ppp) REVERT: 3 248 PHE cc_start: 0.9551 (m-10) cc_final: 0.9325 (m-80) REVERT: 3 300 MET cc_start: 0.9406 (mmp) cc_final: 0.9122 (mmp) REVERT: 3 309 GLU cc_start: 0.9547 (tm-30) cc_final: 0.9248 (tm-30) REVERT: 3 350 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8794 (mm110) REVERT: 3 367 ASP cc_start: 0.9125 (m-30) cc_final: 0.8848 (m-30) REVERT: 3 491 MET cc_start: 0.9442 (ptp) cc_final: 0.9178 (ptp) REVERT: 3 500 LEU cc_start: 0.9372 (tp) cc_final: 0.9159 (pp) REVERT: 4 180 MET cc_start: 0.9299 (tpp) cc_final: 0.9086 (tpp) REVERT: 4 201 GLU cc_start: 0.9374 (pm20) cc_final: 0.8902 (pm20) REVERT: 4 234 MET cc_start: 0.8008 (tmm) cc_final: 0.7195 (tmm) REVERT: 4 279 LEU cc_start: 0.9849 (mm) cc_final: 0.9602 (mt) REVERT: 4 299 ASP cc_start: 0.8513 (t0) cc_final: 0.8241 (t0) REVERT: 4 330 ASP cc_start: 0.9393 (m-30) cc_final: 0.9059 (m-30) REVERT: 4 376 GLN cc_start: 0.8743 (mp10) cc_final: 0.8485 (mp10) REVERT: 5 214 LYS cc_start: 0.8762 (mttt) cc_final: 0.8325 (tppt) REVERT: 5 356 MET cc_start: 0.9393 (ttt) cc_final: 0.9111 (tpp) REVERT: 5 453 GLU cc_start: 0.9377 (tt0) cc_final: 0.8979 (pt0) REVERT: 5 491 MET cc_start: 0.9184 (pmm) cc_final: 0.8666 (pmm) REVERT: 7 56 MET cc_start: 0.9068 (mmp) cc_final: 0.8744 (mmp) REVERT: 7 79 PHE cc_start: 0.9292 (p90) cc_final: 0.8768 (p90) REVERT: 7 192 ASP cc_start: 0.9378 (t70) cc_final: 0.8993 (t70) REVERT: 7 204 LYS cc_start: 0.9686 (mmmt) cc_final: 0.9326 (mtpp) REVERT: 8 78 GLN cc_start: 0.9058 (mt0) cc_final: 0.8709 (mt0) REVERT: 8 207 MET cc_start: 0.8793 (mmm) cc_final: 0.8584 (mmm) REVERT: 9 72 MET cc_start: 0.9391 (tmm) cc_final: 0.9173 (tmm) REVERT: 9 124 LEU cc_start: 0.9521 (tp) cc_final: 0.9224 (tp) REVERT: Q 208 MET cc_start: 0.9089 (mmp) cc_final: 0.8838 (mmm) REVERT: R 12 LEU cc_start: 0.9370 (mt) cc_final: 0.9132 (mt) REVERT: R 16 LYS cc_start: 0.9456 (mttt) cc_final: 0.9199 (mttt) REVERT: R 33 LEU cc_start: 0.9150 (tp) cc_final: 0.8795 (mt) REVERT: R 34 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9100 (mmpt) REVERT: T 103 VAL cc_start: 0.9398 (t) cc_final: 0.9089 (p) REVERT: V 5 THR cc_start: 0.5818 (p) cc_final: 0.5379 (t) REVERT: X 13 ASP cc_start: 0.8981 (p0) cc_final: 0.8252 (p0) REVERT: X 15 ASP cc_start: 0.9348 (m-30) cc_final: 0.8693 (p0) REVERT: X 44 THR cc_start: 0.8954 (p) cc_final: 0.8209 (p) REVERT: X 47 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9177 (pt0) REVERT: 6 61 LEU cc_start: 0.7609 (tt) cc_final: 0.7250 (pp) REVERT: 6 134 ASN cc_start: 0.9387 (m-40) cc_final: 0.9042 (m110) REVERT: U 55 MET cc_start: 0.9130 (tpt) cc_final: 0.8122 (tpp) REVERT: U 65 MET cc_start: 0.6239 (tpt) cc_final: 0.4378 (mtt) REVERT: U 222 ASP cc_start: 0.8500 (p0) cc_final: 0.8192 (p0) REVERT: U 228 MET cc_start: 0.8110 (mtp) cc_final: 0.7843 (mmt) REVERT: U 239 LEU cc_start: 0.9159 (mt) cc_final: 0.8800 (tt) REVERT: U 289 PHE cc_start: 0.8889 (m-10) cc_final: 0.8562 (m-80) REVERT: U 441 MET cc_start: 0.7980 (mmm) cc_final: 0.7393 (mmm) REVERT: d 78 MET cc_start: 0.8988 (tpp) cc_final: 0.8706 (tpt) REVERT: d 171 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8587 (tm-30) REVERT: d 195 LYS cc_start: 0.9635 (ptmm) cc_final: 0.9378 (pttm) REVERT: d 297 HIS cc_start: 0.9381 (t70) cc_final: 0.8982 (t70) REVERT: d 308 ASN cc_start: 0.8729 (t0) cc_final: 0.7814 (t0) REVERT: a 10 MET cc_start: 0.7543 (pmm) cc_final: 0.6888 (pmm) REVERT: a 50 LYS cc_start: 0.9455 (mmtt) cc_final: 0.9252 (pttm) REVERT: a 103 LYS cc_start: 0.9417 (mmpt) cc_final: 0.9028 (mmmt) REVERT: a 362 MET cc_start: 0.8369 (ppp) cc_final: 0.7794 (ppp) REVERT: a 382 GLN cc_start: 0.8596 (tp40) cc_final: 0.7545 (tp-100) REVERT: a 473 ASP cc_start: 0.9088 (t0) cc_final: 0.8401 (m-30) REVERT: a 545 MET cc_start: 0.9208 (mtp) cc_final: 0.7811 (mmm) REVERT: a 546 LYS cc_start: 0.8532 (mttt) cc_final: 0.8133 (ptpp) REVERT: a 599 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7806 (p90) REVERT: a 630 GLU cc_start: 0.9294 (tm-30) cc_final: 0.9022 (pp20) REVERT: a 747 SER cc_start: 0.8632 (t) cc_final: 0.8311 (p) REVERT: a 805 LEU cc_start: 0.9392 (mt) cc_final: 0.9185 (mt) REVERT: c 336 MET cc_start: 0.5188 (mmm) cc_final: 0.4973 (mmm) REVERT: c 439 MET cc_start: 0.9367 (mmp) cc_final: 0.8842 (mmm) REVERT: p 314 MET cc_start: 0.9159 (tpt) cc_final: 0.8904 (tpt) REVERT: p 323 ILE cc_start: 0.9525 (pt) cc_final: 0.9268 (pt) REVERT: 0 61 MET cc_start: 0.8834 (tpp) cc_final: 0.8589 (tpp) REVERT: 0 130 ASP cc_start: 0.8881 (p0) cc_final: 0.8573 (t70) REVERT: 0 458 MET cc_start: 0.8504 (ppp) cc_final: 0.8112 (ppp) REVERT: 0 487 GLU cc_start: 0.9584 (tp30) cc_final: 0.9356 (tp30) REVERT: 0 571 ARG cc_start: 0.9354 (tpt-90) cc_final: 0.8957 (tpt90) REVERT: 0 606 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8948 (pp20) REVERT: f 33 PHE cc_start: 0.9592 (m-80) cc_final: 0.9337 (m-80) REVERT: f 67 TYR cc_start: 0.8662 (t80) cc_final: 0.8452 (t80) REVERT: s 52 ARG cc_start: 0.9386 (ttt-90) cc_final: 0.8836 (mmm-85) REVERT: s 180 GLU cc_start: 0.9496 (tp30) cc_final: 0.9138 (tm-30) REVERT: e 12 ILE cc_start: 0.7940 (pt) cc_final: 0.7704 (pt) REVERT: e 17 TRP cc_start: 0.8118 (m100) cc_final: 0.7899 (m100) outliers start: 11 outliers final: 2 residues processed: 1165 average time/residue: 0.6169 time to fit residues: 1219.1135 Evaluate side-chains 825 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 819 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 7.9990 chunk 644 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 434 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 666 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 405 optimal weight: 0.9980 chunk 495 optimal weight: 20.0000 chunk 771 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 92 GLN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 573 HIS 2 242 GLN 3 209 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 262 ASN 4 288 GLN ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN ** R 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 6 GLN V 10 GLN 6 194 HIS U 72 GLN ** U 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN d 10 ASN d 48 HIS d 108 ASN ** a 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 GLN a 315 ASN a 323 GLN a 541 ASN ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 267 ASN c 391 HIS ** 0 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 430 GLN 0 441 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 68434 Z= 0.238 Angle : 0.627 21.610 92493 Z= 0.331 Chirality : 0.042 0.338 10483 Planarity : 0.005 0.125 11849 Dihedral : 4.550 33.886 9314 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 0.26 % Allowed : 4.36 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.11 (0.09), residues: 8508 helix: 1.13 (0.07), residues: 4841 sheet: -1.20 (0.18), residues: 765 loop : -1.34 (0.12), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP f 21 HIS 0.013 0.001 HIS f 36 PHE 0.040 0.002 PHE p 307 TYR 0.040 0.002 TYR i 68 ARG 0.017 0.001 ARG j 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 996 time to evaluate : 6.117 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 19 MET cc_start: 0.9399 (tmm) cc_final: 0.8828 (ptm) REVERT: b 56 LEU cc_start: 0.9545 (mt) cc_final: 0.9241 (pp) REVERT: b 103 TYR cc_start: 0.8935 (m-10) cc_final: 0.8584 (m-10) REVERT: b 148 ASN cc_start: 0.8666 (t0) cc_final: 0.8445 (t0) REVERT: b 166 ASP cc_start: 0.8327 (t0) cc_final: 0.7842 (t0) REVERT: b 182 PHE cc_start: 0.9213 (m-80) cc_final: 0.8738 (m-80) REVERT: g 36 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8563 (mmmm) REVERT: g 47 MET cc_start: 0.9248 (mmm) cc_final: 0.8324 (mmp) REVERT: g 53 MET cc_start: 0.8546 (mmp) cc_final: 0.8174 (mmp) REVERT: g 115 ASP cc_start: 0.6780 (t70) cc_final: 0.6061 (t0) REVERT: g 123 GLN cc_start: 0.8658 (mp10) cc_final: 0.8218 (mp10) REVERT: g 127 LEU cc_start: 0.9394 (mt) cc_final: 0.8848 (pp) REVERT: h 23 MET cc_start: 0.8782 (tpt) cc_final: 0.8369 (mtt) REVERT: h 28 MET cc_start: 0.8715 (ptm) cc_final: 0.8432 (ptp) REVERT: h 32 TYR cc_start: 0.7452 (m-80) cc_final: 0.7063 (m-80) REVERT: h 53 MET cc_start: 0.6873 (ttt) cc_final: 0.6309 (tmm) REVERT: h 64 ILE cc_start: 0.9639 (mm) cc_final: 0.9390 (mm) REVERT: h 68 TYR cc_start: 0.9403 (m-10) cc_final: 0.9159 (m-10) REVERT: h 127 LEU cc_start: 0.8192 (mt) cc_final: 0.7928 (mt) REVERT: i 134 ILE cc_start: 0.8829 (mm) cc_final: 0.8562 (pt) REVERT: j 25 PHE cc_start: 0.8869 (m-10) cc_final: 0.8552 (m-80) REVERT: j 140 VAL cc_start: 0.9345 (p) cc_final: 0.9091 (m) REVERT: j 143 LEU cc_start: 0.9285 (tp) cc_final: 0.8928 (tp) REVERT: j 147 ILE cc_start: 0.9058 (mt) cc_final: 0.8819 (mt) REVERT: k 53 MET cc_start: 0.6564 (ttt) cc_final: 0.5912 (tpp) REVERT: k 56 ILE cc_start: 0.8029 (tp) cc_final: 0.7815 (mm) REVERT: k 74 VAL cc_start: 0.8575 (m) cc_final: 0.8359 (p) REVERT: k 131 MET cc_start: 0.9048 (ttp) cc_final: 0.8710 (tmm) REVERT: l 28 MET cc_start: 0.7696 (mmp) cc_final: 0.7423 (mmp) REVERT: l 53 MET cc_start: 0.5817 (tmm) cc_final: 0.4952 (tpt) REVERT: l 134 ILE cc_start: 0.7023 (mm) cc_final: 0.6529 (mm) REVERT: l 147 ILE cc_start: 0.8655 (mm) cc_final: 0.8314 (mm) REVERT: m 104 LEU cc_start: 0.9119 (mt) cc_final: 0.8768 (mt) REVERT: n 25 PHE cc_start: 0.9513 (m-80) cc_final: 0.9093 (m-10) REVERT: n 53 MET cc_start: 0.8370 (pmm) cc_final: 0.8145 (pmm) REVERT: n 54 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9272 (tttt) REVERT: n 78 ASN cc_start: 0.7569 (m-40) cc_final: 0.7166 (p0) REVERT: n 115 ASP cc_start: 0.8684 (t0) cc_final: 0.8313 (t0) REVERT: n 131 MET cc_start: 0.8223 (mmp) cc_final: 0.7765 (tpp) REVERT: n 139 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7951 (tp30) REVERT: o 64 ILE cc_start: 0.9103 (pt) cc_final: 0.8586 (pt) REVERT: o 115 ASP cc_start: 0.9202 (t0) cc_final: 0.8991 (m-30) REVERT: o 144 TYR cc_start: 0.8950 (m-10) cc_final: 0.8691 (m-80) REVERT: 1 95 MET cc_start: 0.9367 (tpp) cc_final: 0.9152 (tpp) REVERT: 1 277 CYS cc_start: 0.8609 (t) cc_final: 0.8109 (t) REVERT: 1 318 MET cc_start: 0.9441 (mmp) cc_final: 0.9174 (mmm) REVERT: 1 385 PHE cc_start: 0.9373 (t80) cc_final: 0.9083 (t80) REVERT: 1 416 ASP cc_start: 0.8162 (t0) cc_final: 0.7923 (t70) REVERT: 1 458 MET cc_start: 0.9206 (pmm) cc_final: 0.8949 (pmm) REVERT: 1 461 LEU cc_start: 0.9440 (mt) cc_final: 0.9010 (pp) REVERT: 1 540 MET cc_start: 0.9270 (mtp) cc_final: 0.8688 (mtp) REVERT: 1 550 MET cc_start: 0.9615 (mtp) cc_final: 0.8932 (ttp) REVERT: 1 574 MET cc_start: 0.8931 (mtt) cc_final: 0.8692 (mmt) REVERT: 1 608 MET cc_start: 0.9510 (ptm) cc_final: 0.9211 (ppp) REVERT: 2 318 MET cc_start: 0.9542 (mmp) cc_final: 0.9186 (mmm) REVERT: 2 340 MET cc_start: 0.9155 (ttm) cc_final: 0.8733 (ttm) REVERT: 2 465 TYR cc_start: 0.9300 (m-80) cc_final: 0.9039 (m-80) REVERT: 2 544 MET cc_start: 0.9701 (mtp) cc_final: 0.9366 (mmt) REVERT: 2 550 MET cc_start: 0.9659 (tpt) cc_final: 0.9164 (tpp) REVERT: 2 574 MET cc_start: 0.8391 (mpp) cc_final: 0.8120 (mpp) REVERT: 2 584 MET cc_start: 0.8647 (ppp) cc_final: 0.8329 (ppp) REVERT: 3 154 MET cc_start: 0.9085 (tpp) cc_final: 0.8839 (mmp) REVERT: 3 231 PHE cc_start: 0.8960 (t80) cc_final: 0.8650 (t80) REVERT: 3 238 MET cc_start: 0.9324 (ppp) cc_final: 0.8984 (ppp) REVERT: 3 248 PHE cc_start: 0.9598 (m-10) cc_final: 0.9306 (m-80) REVERT: 3 309 GLU cc_start: 0.9575 (tm-30) cc_final: 0.9303 (tm-30) REVERT: 3 350 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8937 (mm-40) REVERT: 3 367 ASP cc_start: 0.9111 (m-30) cc_final: 0.8863 (m-30) REVERT: 3 378 TYR cc_start: 0.8872 (t80) cc_final: 0.8491 (t80) REVERT: 3 449 LEU cc_start: 0.9755 (tp) cc_final: 0.9468 (pp) REVERT: 3 457 LYS cc_start: 0.9715 (mmtt) cc_final: 0.9515 (mmmt) REVERT: 3 491 MET cc_start: 0.9494 (ptp) cc_final: 0.9192 (ptp) REVERT: 4 180 MET cc_start: 0.9425 (tpp) cc_final: 0.9166 (tpp) REVERT: 4 234 MET cc_start: 0.7995 (tmm) cc_final: 0.6909 (tmm) REVERT: 4 279 LEU cc_start: 0.9889 (mm) cc_final: 0.9626 (mt) REVERT: 4 299 ASP cc_start: 0.8721 (t0) cc_final: 0.8321 (t0) REVERT: 4 330 ASP cc_start: 0.9420 (m-30) cc_final: 0.9118 (m-30) REVERT: 4 356 MET cc_start: 0.8868 (mtm) cc_final: 0.8504 (mtm) REVERT: 4 376 GLN cc_start: 0.8718 (mp10) cc_final: 0.8431 (mp10) REVERT: 4 378 TYR cc_start: 0.9079 (t80) cc_final: 0.8614 (t80) REVERT: 4 402 MET cc_start: 0.9263 (ttm) cc_final: 0.9021 (mmm) REVERT: 4 417 ASP cc_start: 0.9253 (p0) cc_final: 0.8834 (p0) REVERT: 5 214 LYS cc_start: 0.8854 (mttt) cc_final: 0.8400 (tppt) REVERT: 5 270 GLU cc_start: 0.8567 (tp30) cc_final: 0.8293 (tp30) REVERT: 5 356 MET cc_start: 0.9416 (ttt) cc_final: 0.9071 (tpp) REVERT: 5 453 GLU cc_start: 0.9405 (tt0) cc_final: 0.8914 (pt0) REVERT: 5 491 MET cc_start: 0.8961 (pmm) cc_final: 0.8676 (pmm) REVERT: 7 56 MET cc_start: 0.9075 (mmp) cc_final: 0.8730 (mmp) REVERT: 7 79 PHE cc_start: 0.9329 (p90) cc_final: 0.8856 (p90) REVERT: 7 192 ASP cc_start: 0.9402 (t70) cc_final: 0.9036 (t70) REVERT: 7 197 GLU cc_start: 0.8634 (pt0) cc_final: 0.8355 (pt0) REVERT: 7 204 LYS cc_start: 0.9703 (mmmt) cc_final: 0.9358 (mmmt) REVERT: 8 132 MET cc_start: 0.7179 (mmp) cc_final: 0.6841 (mmm) REVERT: 8 207 MET cc_start: 0.8825 (mmm) cc_final: 0.8458 (mmm) REVERT: 9 16 MET cc_start: 0.7206 (mmt) cc_final: 0.6943 (mmm) REVERT: 9 125 TYR cc_start: 0.8444 (m-10) cc_final: 0.8024 (m-80) REVERT: 9 207 MET cc_start: 0.9314 (tpp) cc_final: 0.9091 (tpp) REVERT: V 5 THR cc_start: 0.5757 (p) cc_final: 0.5551 (t) REVERT: X 13 ASP cc_start: 0.9091 (p0) cc_final: 0.8410 (p0) REVERT: X 15 ASP cc_start: 0.9342 (m-30) cc_final: 0.8668 (p0) REVERT: X 44 THR cc_start: 0.9026 (p) cc_final: 0.8036 (t) REVERT: X 47 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9270 (pt0) REVERT: X 57 ASN cc_start: 0.9214 (m110) cc_final: 0.8924 (m-40) REVERT: 6 134 ASN cc_start: 0.9417 (m-40) cc_final: 0.9070 (m110) REVERT: 6 300 LEU cc_start: 0.8176 (mt) cc_final: 0.7975 (mt) REVERT: U 55 MET cc_start: 0.8453 (tpt) cc_final: 0.8100 (tmm) REVERT: U 65 MET cc_start: 0.6341 (tpt) cc_final: 0.4593 (mtt) REVERT: U 239 LEU cc_start: 0.9147 (mt) cc_final: 0.8782 (tt) REVERT: U 289 PHE cc_start: 0.8985 (m-10) cc_final: 0.8689 (m-80) REVERT: U 441 MET cc_start: 0.8057 (mmm) cc_final: 0.7785 (mmm) REVERT: d 145 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7567 (mm-40) REVERT: d 171 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8552 (tm-30) REVERT: d 200 LEU cc_start: 0.9351 (mt) cc_final: 0.9016 (mt) REVERT: d 297 HIS cc_start: 0.9391 (t70) cc_final: 0.9014 (t-90) REVERT: d 308 ASN cc_start: 0.8254 (t0) cc_final: 0.7743 (t0) REVERT: a 10 MET cc_start: 0.7884 (pmm) cc_final: 0.7057 (pmm) REVERT: a 103 LYS cc_start: 0.9481 (mmpt) cc_final: 0.9135 (mmmt) REVERT: a 382 GLN cc_start: 0.8588 (tp40) cc_final: 0.7626 (tp-100) REVERT: a 473 ASP cc_start: 0.9154 (t0) cc_final: 0.8366 (m-30) REVERT: a 546 LYS cc_start: 0.8453 (mttt) cc_final: 0.8003 (ptpp) REVERT: a 747 SER cc_start: 0.8657 (t) cc_final: 0.8347 (p) REVERT: c 439 MET cc_start: 0.9396 (mmp) cc_final: 0.8859 (mmm) REVERT: 0 108 ASP cc_start: 0.9369 (t70) cc_final: 0.9125 (t0) REVERT: 0 130 ASP cc_start: 0.8973 (p0) cc_final: 0.8610 (t70) REVERT: 0 274 TYR cc_start: 0.8571 (t80) cc_final: 0.8358 (t80) REVERT: 0 318 MET cc_start: 0.9486 (mmp) cc_final: 0.9185 (mmm) REVERT: 0 458 MET cc_start: 0.8403 (ppp) cc_final: 0.8066 (ppp) REVERT: 0 571 ARG cc_start: 0.9315 (tpt-90) cc_final: 0.9059 (tpp80) REVERT: f 67 TYR cc_start: 0.8689 (t80) cc_final: 0.8425 (t80) REVERT: s 180 GLU cc_start: 0.9501 (tp30) cc_final: 0.9140 (tm-30) REVERT: s 181 MET cc_start: 0.6252 (tpp) cc_final: 0.5913 (tpp) outliers start: 19 outliers final: 5 residues processed: 1010 average time/residue: 0.6111 time to fit residues: 1061.8386 Evaluate side-chains 775 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 770 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 642 optimal weight: 7.9990 chunk 525 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 773 optimal weight: 9.9990 chunk 835 optimal weight: 8.9990 chunk 688 optimal weight: 20.0000 chunk 766 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 620 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN 1 140 ASN ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 610 ASN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 169 GLN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 HIS 6 254 ASN U 303 GLN U 323 GLN U 379 ASN ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 GLN ** a 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 608 HIS ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 68434 Z= 0.304 Angle : 0.656 10.650 92493 Z= 0.351 Chirality : 0.043 0.254 10483 Planarity : 0.005 0.076 11849 Dihedral : 4.591 30.038 9314 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.35 % Favored : 94.57 % Rotamer: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.16 (0.09), residues: 8508 helix: 1.15 (0.07), residues: 4828 sheet: -0.97 (0.19), residues: 735 loop : -1.31 (0.12), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 2 450 HIS 0.012 0.001 HIS R 111 PHE 0.036 0.002 PHE p 307 TYR 0.029 0.002 TYR g 144 ARG 0.009 0.001 ARG 0 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 909 time to evaluate : 6.091 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: symmetry clash revert: symmetry clash REVERT: b 19 MET cc_start: 0.9384 (tmm) cc_final: 0.8863 (ptp) REVERT: b 107 MET cc_start: 0.9218 (tpp) cc_final: 0.8712 (tmm) REVERT: b 142 LEU cc_start: 0.9132 (tt) cc_final: 0.8784 (tt) REVERT: b 146 LEU cc_start: 0.8927 (mm) cc_final: 0.8704 (mm) REVERT: b 166 ASP cc_start: 0.8541 (t0) cc_final: 0.8112 (t0) REVERT: b 182 PHE cc_start: 0.9244 (m-80) cc_final: 0.8752 (m-80) REVERT: g 36 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8810 (mmmm) REVERT: g 47 MET cc_start: 0.9074 (mmm) cc_final: 0.8368 (mmp) REVERT: g 118 VAL cc_start: 0.9188 (p) cc_final: 0.8912 (p) REVERT: g 123 GLN cc_start: 0.8623 (mp10) cc_final: 0.8265 (mp10) REVERT: g 144 TYR cc_start: 0.9451 (m-80) cc_final: 0.9220 (m-80) REVERT: h 23 MET cc_start: 0.8856 (tpt) cc_final: 0.8445 (mtt) REVERT: h 32 TYR cc_start: 0.7560 (m-80) cc_final: 0.7299 (m-80) REVERT: h 53 MET cc_start: 0.6368 (ttt) cc_final: 0.5870 (tmm) REVERT: h 64 ILE cc_start: 0.9717 (mm) cc_final: 0.9407 (mt) REVERT: h 68 TYR cc_start: 0.9434 (m-10) cc_final: 0.9188 (m-10) REVERT: h 127 LEU cc_start: 0.8373 (mt) cc_final: 0.8050 (mt) REVERT: h 144 TYR cc_start: 0.9688 (m-80) cc_final: 0.9442 (m-80) REVERT: i 144 TYR cc_start: 0.8172 (m-10) cc_final: 0.7815 (m-10) REVERT: j 25 PHE cc_start: 0.8842 (m-10) cc_final: 0.8438 (m-80) REVERT: j 53 MET cc_start: 0.7655 (mmm) cc_final: 0.7305 (tpp) REVERT: j 140 VAL cc_start: 0.9275 (p) cc_final: 0.8911 (m) REVERT: k 53 MET cc_start: 0.6654 (ttt) cc_final: 0.6071 (tpp) REVERT: k 131 MET cc_start: 0.9067 (ttp) cc_final: 0.8683 (tmm) REVERT: l 53 MET cc_start: 0.5735 (tmm) cc_final: 0.5002 (tpt) REVERT: l 112 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7986 (pt) REVERT: m 104 LEU cc_start: 0.9163 (mt) cc_final: 0.8810 (mt) REVERT: n 25 PHE cc_start: 0.9473 (m-80) cc_final: 0.9147 (m-10) REVERT: n 53 MET cc_start: 0.8383 (pmm) cc_final: 0.8125 (pmm) REVERT: n 54 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9254 (tttt) REVERT: n 61 MET cc_start: 0.9112 (ttm) cc_final: 0.8392 (tmm) REVERT: n 78 ASN cc_start: 0.7617 (m-40) cc_final: 0.7182 (p0) REVERT: n 135 LEU cc_start: 0.8489 (mt) cc_final: 0.7396 (tt) REVERT: o 68 TYR cc_start: 0.8643 (m-10) cc_final: 0.8121 (m-10) REVERT: o 115 ASP cc_start: 0.9251 (t0) cc_final: 0.9047 (m-30) REVERT: o 144 TYR cc_start: 0.8843 (m-10) cc_final: 0.8565 (m-80) REVERT: 1 108 ASP cc_start: 0.9503 (m-30) cc_final: 0.9244 (m-30) REVERT: 1 277 CYS cc_start: 0.8698 (t) cc_final: 0.8286 (t) REVERT: 1 318 MET cc_start: 0.9453 (mmp) cc_final: 0.9230 (mmp) REVERT: 1 346 MET cc_start: 0.9008 (ttm) cc_final: 0.8721 (tpp) REVERT: 1 385 PHE cc_start: 0.9399 (t80) cc_final: 0.9176 (t80) REVERT: 1 416 ASP cc_start: 0.8236 (t0) cc_final: 0.8022 (t0) REVERT: 1 458 MET cc_start: 0.9343 (pmm) cc_final: 0.9017 (pmm) REVERT: 1 461 LEU cc_start: 0.9459 (mt) cc_final: 0.9042 (pp) REVERT: 1 540 MET cc_start: 0.9293 (mtp) cc_final: 0.8796 (mtp) REVERT: 1 544 MET cc_start: 0.9406 (mpp) cc_final: 0.9121 (mpp) REVERT: 1 550 MET cc_start: 0.9578 (mtp) cc_final: 0.8982 (ttp) REVERT: 1 574 MET cc_start: 0.9000 (mtt) cc_final: 0.8703 (mmt) REVERT: 1 608 MET cc_start: 0.9318 (ptm) cc_final: 0.9070 (ppp) REVERT: 2 263 LEU cc_start: 0.9818 (tp) cc_final: 0.9610 (pp) REVERT: 2 318 MET cc_start: 0.9563 (mmp) cc_final: 0.9171 (mmm) REVERT: 2 340 MET cc_start: 0.9125 (ttm) cc_final: 0.8688 (ttm) REVERT: 2 346 MET cc_start: 0.9045 (tpt) cc_final: 0.8501 (tpp) REVERT: 2 382 LEU cc_start: 0.9713 (tp) cc_final: 0.9502 (tt) REVERT: 2 544 MET cc_start: 0.9723 (mtp) cc_final: 0.9356 (mmt) REVERT: 2 550 MET cc_start: 0.9672 (tpt) cc_final: 0.9140 (tpp) REVERT: 2 574 MET cc_start: 0.8494 (mpp) cc_final: 0.8152 (mpp) REVERT: 3 231 PHE cc_start: 0.9079 (t80) cc_final: 0.8738 (t80) REVERT: 3 238 MET cc_start: 0.9339 (ppp) cc_final: 0.8977 (ppp) REVERT: 3 248 PHE cc_start: 0.9663 (m-10) cc_final: 0.9361 (m-80) REVERT: 3 300 MET cc_start: 0.9467 (mmp) cc_final: 0.9033 (mmp) REVERT: 3 309 GLU cc_start: 0.9570 (tm-30) cc_final: 0.9283 (tm-30) REVERT: 3 350 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8954 (mm-40) REVERT: 3 367 ASP cc_start: 0.9048 (m-30) cc_final: 0.8792 (m-30) REVERT: 3 435 MET cc_start: 0.9219 (mtm) cc_final: 0.8976 (ptp) REVERT: 3 449 LEU cc_start: 0.9753 (tp) cc_final: 0.9492 (pp) REVERT: 4 97 GLN cc_start: 0.9230 (pt0) cc_final: 0.8885 (pm20) REVERT: 4 180 MET cc_start: 0.9484 (tpp) cc_final: 0.9206 (tpp) REVERT: 4 187 GLN cc_start: 0.8083 (tt0) cc_final: 0.7499 (tm-30) REVERT: 4 234 MET cc_start: 0.7979 (tmm) cc_final: 0.7298 (tmm) REVERT: 4 299 ASP cc_start: 0.8869 (t0) cc_final: 0.8551 (t0) REVERT: 4 356 MET cc_start: 0.8879 (mtm) cc_final: 0.8510 (mtm) REVERT: 4 376 GLN cc_start: 0.8840 (mp10) cc_final: 0.8542 (mp10) REVERT: 4 378 TYR cc_start: 0.9303 (t80) cc_final: 0.8972 (t80) REVERT: 4 417 ASP cc_start: 0.9290 (p0) cc_final: 0.8867 (p0) REVERT: 4 459 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9185 (pp20) REVERT: 5 214 LYS cc_start: 0.8847 (mttt) cc_final: 0.8366 (tppt) REVERT: 5 270 GLU cc_start: 0.8711 (tp30) cc_final: 0.8411 (tp30) REVERT: 5 356 MET cc_start: 0.9356 (ttt) cc_final: 0.9028 (tpp) REVERT: 5 453 GLU cc_start: 0.9446 (tt0) cc_final: 0.8950 (pt0) REVERT: 7 56 MET cc_start: 0.9062 (mmp) cc_final: 0.8703 (mmp) REVERT: 7 192 ASP cc_start: 0.9470 (t70) cc_final: 0.9190 (t70) REVERT: 7 204 LYS cc_start: 0.9704 (mmmt) cc_final: 0.9357 (mmmt) REVERT: 8 132 MET cc_start: 0.7396 (mmp) cc_final: 0.6892 (mmm) REVERT: 9 16 MET cc_start: 0.7800 (mmm) cc_final: 0.7180 (mmm) REVERT: 9 207 MET cc_start: 0.9379 (tpp) cc_final: 0.9170 (tpp) REVERT: T 42 MET cc_start: 0.9566 (mtm) cc_final: 0.9286 (ppp) REVERT: V 5 THR cc_start: 0.5727 (p) cc_final: 0.5514 (t) REVERT: X 44 THR cc_start: 0.9060 (p) cc_final: 0.7971 (t) REVERT: X 47 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9244 (pt0) REVERT: X 57 ASN cc_start: 0.9256 (m110) cc_final: 0.8957 (m-40) REVERT: 6 23 HIS cc_start: 0.8576 (t-170) cc_final: 0.8321 (t-170) REVERT: 6 134 ASN cc_start: 0.9420 (m-40) cc_final: 0.9026 (m110) REVERT: U 65 MET cc_start: 0.6555 (tpt) cc_final: 0.4616 (mtt) REVERT: U 239 LEU cc_start: 0.9162 (mt) cc_final: 0.8836 (tt) REVERT: U 289 PHE cc_start: 0.9063 (m-10) cc_final: 0.8716 (m-80) REVERT: d 44 ASP cc_start: 0.9584 (m-30) cc_final: 0.9240 (m-30) REVERT: d 105 MET cc_start: 0.9114 (tpp) cc_final: 0.8844 (tpt) REVERT: d 124 GLU cc_start: 0.8952 (mp0) cc_final: 0.8739 (pm20) REVERT: d 171 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8137 (tm-30) REVERT: d 194 TYR cc_start: 0.9159 (t80) cc_final: 0.8940 (t80) REVERT: d 297 HIS cc_start: 0.9429 (t70) cc_final: 0.9070 (t70) REVERT: d 308 ASN cc_start: 0.8324 (t0) cc_final: 0.7826 (t0) REVERT: a 10 MET cc_start: 0.7910 (pmm) cc_final: 0.7125 (pmm) REVERT: a 103 LYS cc_start: 0.9530 (mmpt) cc_final: 0.9192 (mmmt) REVERT: a 408 PHE cc_start: 0.8872 (p90) cc_final: 0.8535 (p90) REVERT: a 430 MET cc_start: 0.8503 (mmp) cc_final: 0.8279 (mmm) REVERT: a 546 LYS cc_start: 0.8256 (mttt) cc_final: 0.7783 (mttp) REVERT: a 747 SER cc_start: 0.8610 (t) cc_final: 0.8248 (m) REVERT: a 805 LEU cc_start: 0.9394 (mt) cc_final: 0.9141 (mt) REVERT: a 809 TRP cc_start: 0.8746 (t60) cc_final: 0.8280 (t60) REVERT: c 439 MET cc_start: 0.9509 (mmp) cc_final: 0.8973 (mmm) REVERT: 0 108 ASP cc_start: 0.9376 (t70) cc_final: 0.9170 (t0) REVERT: 0 340 MET cc_start: 0.8736 (tpp) cc_final: 0.8490 (tpp) REVERT: s 180 GLU cc_start: 0.9511 (tp30) cc_final: 0.9171 (tm-30) REVERT: s 181 MET cc_start: 0.6339 (tpp) cc_final: 0.6016 (tpp) REVERT: s 183 MET cc_start: 0.5092 (ptt) cc_final: 0.4608 (ptt) outliers start: 8 outliers final: 2 residues processed: 917 average time/residue: 0.6377 time to fit residues: 1018.0796 Evaluate side-chains 709 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 705 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 9.9990 chunk 581 optimal weight: 0.9980 chunk 401 optimal weight: 7.9990 chunk 85 optimal weight: 0.2980 chunk 369 optimal weight: 2.9990 chunk 519 optimal weight: 5.9990 chunk 776 optimal weight: 5.9990 chunk 821 optimal weight: 5.9990 chunk 405 optimal weight: 0.9990 chunk 735 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 282 ASN ** 1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 181 ASN 4 358 ASN 5 209 GLN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 323 GLN U 405 GLN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 382 GLN ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 189 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 68434 Z= 0.194 Angle : 0.612 10.557 92493 Z= 0.320 Chirality : 0.042 0.246 10483 Planarity : 0.004 0.068 11849 Dihedral : 4.469 30.846 9314 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.40 (0.09), residues: 8508 helix: 1.32 (0.07), residues: 4808 sheet: -0.65 (0.19), residues: 756 loop : -1.22 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP f 21 HIS 0.006 0.001 HIS R 111 PHE 0.031 0.002 PHE Q 18 TYR 0.034 0.001 TYR b 135 ARG 0.010 0.000 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 947 time to evaluate : 6.188 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: symmetry clash revert: symmetry clash revert: 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 19 MET cc_start: 0.9351 (tmm) cc_final: 0.8859 (ptp) REVERT: b 103 TYR cc_start: 0.8776 (m-10) cc_final: 0.8558 (m-10) REVERT: b 107 MET cc_start: 0.9203 (tpp) cc_final: 0.8683 (tmm) REVERT: b 142 LEU cc_start: 0.9124 (tt) cc_final: 0.8769 (tt) REVERT: b 146 LEU cc_start: 0.8966 (mm) cc_final: 0.8680 (mm) REVERT: b 148 ASN cc_start: 0.8547 (t0) cc_final: 0.8221 (t0) REVERT: b 166 ASP cc_start: 0.8473 (t0) cc_final: 0.8098 (t0) REVERT: b 182 PHE cc_start: 0.9182 (m-80) cc_final: 0.8731 (m-80) REVERT: g 36 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8620 (mmmm) REVERT: g 47 MET cc_start: 0.9054 (mmm) cc_final: 0.8351 (mmp) REVERT: g 48 ARG cc_start: 0.9116 (mmp80) cc_final: 0.8915 (mmp80) REVERT: g 115 ASP cc_start: 0.6589 (t70) cc_final: 0.5249 (t0) REVERT: g 123 GLN cc_start: 0.8651 (mp10) cc_final: 0.8232 (mp10) REVERT: h 23 MET cc_start: 0.8835 (tpt) cc_final: 0.8412 (mtt) REVERT: h 32 TYR cc_start: 0.7419 (m-80) cc_final: 0.7121 (m-80) REVERT: h 53 MET cc_start: 0.5959 (ttt) cc_final: 0.5456 (tmm) REVERT: h 64 ILE cc_start: 0.9676 (mm) cc_final: 0.9459 (mm) REVERT: h 68 TYR cc_start: 0.9396 (m-10) cc_final: 0.9168 (m-10) REVERT: h 127 LEU cc_start: 0.8399 (mt) cc_final: 0.8035 (mt) REVERT: h 131 MET cc_start: 0.9122 (ptp) cc_final: 0.8837 (ptp) REVERT: h 144 TYR cc_start: 0.9694 (m-80) cc_final: 0.9439 (m-80) REVERT: i 144 TYR cc_start: 0.8185 (m-10) cc_final: 0.7781 (m-10) REVERT: j 25 PHE cc_start: 0.8803 (m-10) cc_final: 0.8493 (m-80) REVERT: j 53 MET cc_start: 0.7612 (mmm) cc_final: 0.7252 (tpp) REVERT: j 92 GLN cc_start: 0.8171 (mp10) cc_final: 0.7420 (mm-40) REVERT: j 140 VAL cc_start: 0.9291 (p) cc_final: 0.8852 (m) REVERT: k 53 MET cc_start: 0.6853 (ttt) cc_final: 0.6222 (tpp) REVERT: k 61 MET cc_start: 0.7635 (ppp) cc_final: 0.7245 (ppp) REVERT: k 74 VAL cc_start: 0.8672 (m) cc_final: 0.8455 (p) REVERT: k 131 MET cc_start: 0.9099 (ttp) cc_final: 0.8695 (tmm) REVERT: l 28 MET cc_start: 0.7621 (mmp) cc_final: 0.7394 (mmp) REVERT: l 53 MET cc_start: 0.6351 (tmm) cc_final: 0.5583 (tpt) REVERT: l 131 MET cc_start: 0.8597 (tpp) cc_final: 0.8346 (tpt) REVERT: l 147 ILE cc_start: 0.8713 (mm) cc_final: 0.8504 (mm) REVERT: m 61 MET cc_start: 0.8486 (mmt) cc_final: 0.8140 (mmt) REVERT: m 104 LEU cc_start: 0.9163 (mt) cc_final: 0.8795 (mt) REVERT: n 25 PHE cc_start: 0.9499 (m-80) cc_final: 0.9039 (m-10) REVERT: n 53 MET cc_start: 0.8351 (pmm) cc_final: 0.8078 (pmm) REVERT: n 54 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9221 (mtpt) REVERT: n 78 ASN cc_start: 0.7568 (m-40) cc_final: 0.7173 (p0) REVERT: n 131 MET cc_start: 0.8383 (mmp) cc_final: 0.7738 (mmt) REVERT: o 68 TYR cc_start: 0.8603 (m-10) cc_final: 0.8090 (m-10) REVERT: o 144 TYR cc_start: 0.8817 (m-10) cc_final: 0.8583 (m-80) REVERT: 1 34 MET cc_start: 0.9025 (tpp) cc_final: 0.8660 (tpp) REVERT: 1 95 MET cc_start: 0.9372 (tpp) cc_final: 0.9065 (tpp) REVERT: 1 234 LEU cc_start: 0.9058 (mp) cc_final: 0.8772 (mt) REVERT: 1 277 CYS cc_start: 0.8671 (t) cc_final: 0.7939 (t) REVERT: 1 318 MET cc_start: 0.9479 (mmp) cc_final: 0.9179 (mmm) REVERT: 1 346 MET cc_start: 0.8981 (ttm) cc_final: 0.8729 (tpp) REVERT: 1 350 SER cc_start: 0.9116 (m) cc_final: 0.8754 (p) REVERT: 1 385 PHE cc_start: 0.9374 (t80) cc_final: 0.9172 (t80) REVERT: 1 416 ASP cc_start: 0.8182 (t0) cc_final: 0.7963 (t0) REVERT: 1 458 MET cc_start: 0.9367 (pmm) cc_final: 0.9141 (pmm) REVERT: 1 461 LEU cc_start: 0.9428 (mt) cc_final: 0.9022 (pp) REVERT: 1 540 MET cc_start: 0.9232 (mtp) cc_final: 0.8738 (mtp) REVERT: 1 544 MET cc_start: 0.9383 (mpp) cc_final: 0.9149 (mpp) REVERT: 1 550 MET cc_start: 0.9617 (mtp) cc_final: 0.9114 (ttp) REVERT: 1 574 MET cc_start: 0.8922 (mtt) cc_final: 0.8668 (mmt) REVERT: 1 608 MET cc_start: 0.9357 (ptm) cc_final: 0.9098 (ppp) REVERT: 2 306 MET cc_start: 0.9465 (tmm) cc_final: 0.9247 (tmm) REVERT: 2 318 MET cc_start: 0.9483 (mmp) cc_final: 0.9074 (mmm) REVERT: 2 340 MET cc_start: 0.9095 (ttm) cc_final: 0.8635 (ttm) REVERT: 2 346 MET cc_start: 0.9122 (tpt) cc_final: 0.8575 (tpp) REVERT: 2 465 TYR cc_start: 0.9241 (m-80) cc_final: 0.8997 (m-80) REVERT: 2 544 MET cc_start: 0.9695 (mtp) cc_final: 0.9335 (mmt) REVERT: 2 550 MET cc_start: 0.9672 (tpt) cc_final: 0.9139 (tpp) REVERT: 2 574 MET cc_start: 0.8464 (mpp) cc_final: 0.8140 (mpp) REVERT: 2 584 MET cc_start: 0.8588 (ppp) cc_final: 0.8370 (ppp) REVERT: 3 231 PHE cc_start: 0.8993 (t80) cc_final: 0.8748 (t80) REVERT: 3 238 MET cc_start: 0.9269 (ppp) cc_final: 0.8968 (ppp) REVERT: 3 248 PHE cc_start: 0.9625 (m-10) cc_final: 0.9343 (m-80) REVERT: 3 300 MET cc_start: 0.9453 (mmp) cc_final: 0.9251 (mmt) REVERT: 3 309 GLU cc_start: 0.9568 (tm-30) cc_final: 0.9292 (tm-30) REVERT: 3 350 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8949 (mm-40) REVERT: 3 402 MET cc_start: 0.8526 (mmt) cc_final: 0.8299 (mmt) REVERT: 3 449 LEU cc_start: 0.9740 (tp) cc_final: 0.9462 (pp) REVERT: 4 97 GLN cc_start: 0.9179 (pt0) cc_final: 0.8915 (pm20) REVERT: 4 180 MET cc_start: 0.9500 (tpp) cc_final: 0.9243 (tpp) REVERT: 4 187 GLN cc_start: 0.7914 (tt0) cc_final: 0.7175 (tm-30) REVERT: 4 234 MET cc_start: 0.8131 (tmm) cc_final: 0.7033 (tmm) REVERT: 4 279 LEU cc_start: 0.9894 (mm) cc_final: 0.9332 (mt) REVERT: 4 283 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8979 (mp0) REVERT: 4 299 ASP cc_start: 0.8780 (t0) cc_final: 0.8358 (t0) REVERT: 4 330 ASP cc_start: 0.9386 (m-30) cc_final: 0.9177 (m-30) REVERT: 4 356 MET cc_start: 0.8881 (mtm) cc_final: 0.8467 (mtm) REVERT: 4 378 TYR cc_start: 0.9316 (t80) cc_final: 0.8969 (t80) REVERT: 4 417 ASP cc_start: 0.9192 (p0) cc_final: 0.8650 (p0) REVERT: 5 214 LYS cc_start: 0.8848 (mttt) cc_final: 0.8372 (tppt) REVERT: 5 270 GLU cc_start: 0.8640 (tp30) cc_final: 0.8360 (tp30) REVERT: 5 283 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9264 (pt0) REVERT: 5 356 MET cc_start: 0.9325 (ttt) cc_final: 0.9053 (tpp) REVERT: 5 453 GLU cc_start: 0.9431 (tt0) cc_final: 0.9044 (pt0) REVERT: 5 491 MET cc_start: 0.8968 (pmm) cc_final: 0.8726 (pmm) REVERT: 7 56 MET cc_start: 0.9045 (mmp) cc_final: 0.8682 (mmp) REVERT: 7 79 PHE cc_start: 0.9285 (p90) cc_final: 0.8791 (p90) REVERT: 7 204 LYS cc_start: 0.9709 (mmmt) cc_final: 0.9360 (mmmt) REVERT: 8 132 MET cc_start: 0.7330 (mmp) cc_final: 0.6826 (mmm) REVERT: 9 207 MET cc_start: 0.9407 (tpp) cc_final: 0.9123 (tpp) REVERT: X 44 THR cc_start: 0.9089 (p) cc_final: 0.8028 (t) REVERT: X 47 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9309 (pt0) REVERT: X 57 ASN cc_start: 0.9250 (m110) cc_final: 0.8942 (m-40) REVERT: 6 23 HIS cc_start: 0.8521 (t-170) cc_final: 0.8280 (t-170) REVERT: 6 61 LEU cc_start: 0.7763 (tt) cc_final: 0.7295 (pp) REVERT: 6 134 ASN cc_start: 0.9383 (m-40) cc_final: 0.8977 (m110) REVERT: U 65 MET cc_start: 0.6443 (tpt) cc_final: 0.4615 (mtt) REVERT: U 129 MET cc_start: 0.5649 (mpp) cc_final: 0.5427 (mpp) REVERT: U 239 LEU cc_start: 0.9157 (mt) cc_final: 0.8832 (tt) REVERT: U 289 PHE cc_start: 0.9060 (m-10) cc_final: 0.8712 (m-80) REVERT: d 44 ASP cc_start: 0.9580 (m-30) cc_final: 0.9320 (t0) REVERT: d 48 HIS cc_start: 0.8846 (m-70) cc_final: 0.8611 (m-70) REVERT: d 200 LEU cc_start: 0.9333 (mt) cc_final: 0.9041 (mt) REVERT: d 297 HIS cc_start: 0.9410 (t70) cc_final: 0.9013 (t70) REVERT: a 10 MET cc_start: 0.7697 (pmm) cc_final: 0.6970 (pmm) REVERT: a 362 MET cc_start: 0.8173 (ppp) cc_final: 0.7311 (ppp) REVERT: a 408 PHE cc_start: 0.8810 (p90) cc_final: 0.8509 (p90) REVERT: a 430 MET cc_start: 0.8516 (mmp) cc_final: 0.8184 (mmm) REVERT: a 546 LYS cc_start: 0.8168 (mttt) cc_final: 0.7750 (mttp) REVERT: a 635 MET cc_start: 0.4158 (tmm) cc_final: 0.3933 (tmm) REVERT: a 746 LEU cc_start: 0.9311 (tt) cc_final: 0.9003 (tt) REVERT: a 747 SER cc_start: 0.8564 (t) cc_final: 0.7712 (m) REVERT: a 809 TRP cc_start: 0.8648 (t60) cc_final: 0.8334 (t60) REVERT: a 823 LYS cc_start: 0.9460 (tptp) cc_final: 0.9254 (tptt) REVERT: c 388 MET cc_start: 0.8458 (tmm) cc_final: 0.8192 (tmm) REVERT: c 439 MET cc_start: 0.9539 (mmp) cc_final: 0.9047 (mmm) REVERT: 0 39 MET cc_start: 0.8171 (tmm) cc_final: 0.7923 (tmm) REVERT: 0 108 ASP cc_start: 0.9346 (t70) cc_final: 0.9138 (t0) REVERT: 0 130 ASP cc_start: 0.9197 (m-30) cc_final: 0.8594 (t70) REVERT: 0 318 MET cc_start: 0.9465 (mmp) cc_final: 0.9161 (mmm) REVERT: 0 340 MET cc_start: 0.8809 (tpp) cc_final: 0.8216 (tpp) REVERT: 0 472 PHE cc_start: 0.9152 (t80) cc_final: 0.8886 (t80) REVERT: f 67 TYR cc_start: 0.8829 (m-80) cc_final: 0.8371 (t80) REVERT: f 70 PHE cc_start: 0.8973 (m-10) cc_final: 0.8642 (m-10) REVERT: s 180 GLU cc_start: 0.9505 (tp30) cc_final: 0.9142 (tm-30) REVERT: s 181 MET cc_start: 0.6308 (tpp) cc_final: 0.5952 (tpp) REVERT: s 183 MET cc_start: 0.5186 (ptt) cc_final: 0.4658 (ptt) outliers start: 2 outliers final: 1 residues processed: 949 average time/residue: 0.6019 time to fit residues: 990.2585 Evaluate side-chains 735 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 734 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 8.9990 chunk 466 optimal weight: 8.9990 chunk 11 optimal weight: 40.0000 chunk 611 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 701 optimal weight: 10.0000 chunk 567 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 737 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 7 ASN ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 231 GLN ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 187 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 152 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 HIS ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 68434 Z= 0.319 Angle : 0.673 12.319 92493 Z= 0.359 Chirality : 0.043 0.289 10483 Planarity : 0.005 0.077 11849 Dihedral : 4.626 29.312 9314 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.14 % Favored : 93.79 % Rotamer: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.20 (0.09), residues: 8508 helix: 1.15 (0.07), residues: 4786 sheet: -0.63 (0.20), residues: 729 loop : -1.31 (0.12), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 2 450 HIS 0.011 0.001 HIS R 111 PHE 0.042 0.002 PHE s 107 TYR 0.041 0.002 TYR b 70 ARG 0.010 0.001 ARG 8 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 870 time to evaluate : 6.137 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: b 19 MET cc_start: 0.9367 (tmm) cc_final: 0.8837 (ptp) REVERT: b 142 LEU cc_start: 0.9135 (tt) cc_final: 0.8827 (tt) REVERT: b 146 LEU cc_start: 0.8960 (mm) cc_final: 0.8727 (mm) REVERT: b 148 ASN cc_start: 0.8537 (t0) cc_final: 0.8201 (t0) REVERT: b 166 ASP cc_start: 0.8592 (t0) cc_final: 0.8235 (t0) REVERT: b 182 PHE cc_start: 0.9232 (m-80) cc_final: 0.8751 (m-80) REVERT: g 36 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8633 (mmmm) REVERT: g 47 MET cc_start: 0.9040 (mmm) cc_final: 0.8786 (mmp) REVERT: g 123 GLN cc_start: 0.8811 (mp10) cc_final: 0.8428 (mp10) REVERT: h 23 MET cc_start: 0.8931 (tpt) cc_final: 0.8499 (mtt) REVERT: h 53 MET cc_start: 0.5924 (ttt) cc_final: 0.5477 (tmm) REVERT: h 64 ILE cc_start: 0.9668 (mm) cc_final: 0.9382 (mt) REVERT: h 68 TYR cc_start: 0.9414 (m-10) cc_final: 0.9153 (m-10) REVERT: h 127 LEU cc_start: 0.8532 (mt) cc_final: 0.8182 (mt) REVERT: h 144 TYR cc_start: 0.9712 (m-80) cc_final: 0.9450 (m-80) REVERT: i 44 MET cc_start: 0.8085 (tpt) cc_final: 0.7367 (ttt) REVERT: i 131 MET cc_start: 0.7828 (mmt) cc_final: 0.7572 (mmt) REVERT: i 134 ILE cc_start: 0.8848 (mm) cc_final: 0.8646 (pt) REVERT: i 144 TYR cc_start: 0.8125 (m-10) cc_final: 0.7734 (m-10) REVERT: j 25 PHE cc_start: 0.8859 (m-10) cc_final: 0.8534 (m-80) REVERT: j 53 MET cc_start: 0.7592 (mmm) cc_final: 0.7266 (tpp) REVERT: j 67 ILE cc_start: 0.8587 (mm) cc_final: 0.8363 (mm) REVERT: j 140 VAL cc_start: 0.9325 (p) cc_final: 0.8899 (m) REVERT: k 53 MET cc_start: 0.6822 (ttt) cc_final: 0.6598 (ttt) REVERT: k 61 MET cc_start: 0.7752 (ppp) cc_final: 0.7313 (ppp) REVERT: k 131 MET cc_start: 0.9015 (ttp) cc_final: 0.8712 (tmm) REVERT: l 28 MET cc_start: 0.7593 (mmp) cc_final: 0.7333 (mmp) REVERT: l 53 MET cc_start: 0.6356 (tmm) cc_final: 0.5606 (tpt) REVERT: l 147 ILE cc_start: 0.8749 (mm) cc_final: 0.8529 (mm) REVERT: m 104 LEU cc_start: 0.9221 (mt) cc_final: 0.8858 (mt) REVERT: m 119 ARG cc_start: 0.8855 (mmt-90) cc_final: 0.8616 (mmt-90) REVERT: m 143 LEU cc_start: 0.9211 (mm) cc_final: 0.9007 (mm) REVERT: n 25 PHE cc_start: 0.9471 (m-80) cc_final: 0.9175 (m-10) REVERT: n 53 MET cc_start: 0.8374 (pmm) cc_final: 0.8121 (pmm) REVERT: n 54 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9263 (mtpt) REVERT: n 78 ASN cc_start: 0.7675 (m-40) cc_final: 0.7464 (m-40) REVERT: o 47 MET cc_start: 0.8604 (ttp) cc_final: 0.7860 (tmm) REVERT: o 68 TYR cc_start: 0.8747 (m-10) cc_final: 0.8228 (m-80) REVERT: o 144 TYR cc_start: 0.8864 (m-10) cc_final: 0.8648 (m-80) REVERT: 1 34 MET cc_start: 0.8891 (tpp) cc_final: 0.8496 (tpp) REVERT: 1 108 ASP cc_start: 0.9517 (m-30) cc_final: 0.9279 (m-30) REVERT: 1 274 TYR cc_start: 0.9115 (t80) cc_final: 0.8905 (t80) REVERT: 1 277 CYS cc_start: 0.8715 (t) cc_final: 0.8393 (t) REVERT: 1 318 MET cc_start: 0.9481 (mmp) cc_final: 0.9223 (mmp) REVERT: 1 340 MET cc_start: 0.8731 (tpp) cc_final: 0.8525 (tpp) REVERT: 1 416 ASP cc_start: 0.8516 (t0) cc_final: 0.8269 (t0) REVERT: 1 540 MET cc_start: 0.9235 (mtp) cc_final: 0.8759 (mtp) REVERT: 1 544 MET cc_start: 0.9398 (mpp) cc_final: 0.9163 (mpp) REVERT: 1 550 MET cc_start: 0.9602 (mtp) cc_final: 0.8960 (ttp) REVERT: 1 574 MET cc_start: 0.8947 (mtt) cc_final: 0.8663 (mmt) REVERT: 1 608 MET cc_start: 0.9379 (ptm) cc_final: 0.9111 (ppp) REVERT: 2 263 LEU cc_start: 0.9817 (tp) cc_final: 0.9601 (pp) REVERT: 2 306 MET cc_start: 0.9474 (tmm) cc_final: 0.9261 (tmm) REVERT: 2 318 MET cc_start: 0.9487 (mmp) cc_final: 0.8995 (mmm) REVERT: 2 340 MET cc_start: 0.9113 (ttm) cc_final: 0.8699 (ttm) REVERT: 2 346 MET cc_start: 0.9208 (tpt) cc_final: 0.8741 (tpp) REVERT: 2 382 LEU cc_start: 0.9780 (tt) cc_final: 0.9571 (pp) REVERT: 2 544 MET cc_start: 0.9724 (mtp) cc_final: 0.9353 (mmt) REVERT: 2 550 MET cc_start: 0.9660 (tpt) cc_final: 0.9106 (tpp) REVERT: 2 574 MET cc_start: 0.8324 (mpp) cc_final: 0.7824 (mpp) REVERT: 3 127 MET cc_start: 0.9268 (tpp) cc_final: 0.8972 (tpp) REVERT: 3 231 PHE cc_start: 0.9110 (t80) cc_final: 0.8871 (t80) REVERT: 3 238 MET cc_start: 0.9296 (ppp) cc_final: 0.9023 (ppp) REVERT: 3 248 PHE cc_start: 0.9642 (m-10) cc_final: 0.9336 (m-80) REVERT: 3 300 MET cc_start: 0.9543 (mmp) cc_final: 0.9044 (mmp) REVERT: 3 309 GLU cc_start: 0.9607 (tm-30) cc_final: 0.9367 (tm-30) REVERT: 3 350 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9130 (mm-40) REVERT: 3 402 MET cc_start: 0.8799 (mmt) cc_final: 0.8517 (mmt) REVERT: 3 449 LEU cc_start: 0.9755 (tp) cc_final: 0.9500 (pp) REVERT: 4 97 GLN cc_start: 0.9248 (pt0) cc_final: 0.8955 (pm20) REVERT: 4 180 MET cc_start: 0.9501 (tpp) cc_final: 0.9238 (tpp) REVERT: 4 187 GLN cc_start: 0.7999 (tt0) cc_final: 0.7133 (tm-30) REVERT: 4 234 MET cc_start: 0.7985 (tmm) cc_final: 0.7249 (tmm) REVERT: 4 283 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8959 (mt-10) REVERT: 4 299 ASP cc_start: 0.8914 (t0) cc_final: 0.8614 (t0) REVERT: 4 356 MET cc_start: 0.8839 (mtm) cc_final: 0.8457 (mtm) REVERT: 4 378 TYR cc_start: 0.9427 (t80) cc_final: 0.9185 (t80) REVERT: 5 214 LYS cc_start: 0.8830 (mttt) cc_final: 0.8337 (tppt) REVERT: 5 270 GLU cc_start: 0.8761 (tp30) cc_final: 0.8488 (tp30) REVERT: 5 283 GLU cc_start: 0.9550 (mt-10) cc_final: 0.9294 (mp0) REVERT: 5 356 MET cc_start: 0.9304 (ttt) cc_final: 0.8998 (tpp) REVERT: 5 453 GLU cc_start: 0.9463 (tt0) cc_final: 0.9127 (tm-30) REVERT: 7 56 MET cc_start: 0.9105 (mmp) cc_final: 0.8715 (mmp) REVERT: 7 152 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9078 (pp30) REVERT: 8 132 MET cc_start: 0.7420 (mmp) cc_final: 0.6759 (mmm) REVERT: X 44 THR cc_start: 0.9084 (p) cc_final: 0.8199 (t) REVERT: X 46 ASN cc_start: 0.9293 (p0) cc_final: 0.9045 (p0) REVERT: X 47 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9338 (pt0) REVERT: X 57 ASN cc_start: 0.9262 (m110) cc_final: 0.8945 (m-40) REVERT: 6 23 HIS cc_start: 0.8721 (t-170) cc_final: 0.8424 (t-170) REVERT: 6 61 LEU cc_start: 0.7787 (tt) cc_final: 0.7530 (tt) REVERT: 6 134 ASN cc_start: 0.9402 (m-40) cc_final: 0.9016 (m110) REVERT: U 55 MET cc_start: 0.8856 (ppp) cc_final: 0.8595 (ppp) REVERT: U 65 MET cc_start: 0.6373 (tpt) cc_final: 0.4352 (mtt) REVERT: U 239 LEU cc_start: 0.9186 (mt) cc_final: 0.8869 (tt) REVERT: U 289 PHE cc_start: 0.9224 (m-10) cc_final: 0.8860 (m-80) REVERT: d 171 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8473 (tm-30) REVERT: d 297 HIS cc_start: 0.9452 (t70) cc_final: 0.9232 (t-90) REVERT: a 406 PHE cc_start: 0.8957 (t80) cc_final: 0.8716 (t80) REVERT: a 430 MET cc_start: 0.8514 (mmp) cc_final: 0.8174 (mmm) REVERT: a 546 LYS cc_start: 0.8430 (mttt) cc_final: 0.8040 (mttp) REVERT: a 746 LEU cc_start: 0.9476 (tt) cc_final: 0.9273 (tt) REVERT: a 747 SER cc_start: 0.8612 (t) cc_final: 0.8004 (m) REVERT: a 809 TRP cc_start: 0.8741 (t60) cc_final: 0.8237 (t60) REVERT: a 823 LYS cc_start: 0.9471 (tptp) cc_final: 0.9263 (tptt) REVERT: c 439 MET cc_start: 0.9613 (mmp) cc_final: 0.9168 (mmm) REVERT: 0 347 MET cc_start: 0.9263 (tpt) cc_final: 0.9048 (tpp) REVERT: f 67 TYR cc_start: 0.8887 (m-80) cc_final: 0.8522 (t80) REVERT: f 70 PHE cc_start: 0.8942 (m-10) cc_final: 0.8700 (m-10) REVERT: s 180 GLU cc_start: 0.9524 (tp30) cc_final: 0.9171 (tm-30) REVERT: s 181 MET cc_start: 0.6381 (tpp) cc_final: 0.6018 (tpp) REVERT: s 183 MET cc_start: 0.5584 (ptt) cc_final: 0.5010 (ptt) outliers start: 4 outliers final: 2 residues processed: 874 average time/residue: 0.5928 time to fit residues: 899.2636 Evaluate side-chains 694 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 691 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 7.9990 chunk 739 optimal weight: 0.5980 chunk 162 optimal weight: 0.1980 chunk 482 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 822 optimal weight: 0.8980 chunk 682 optimal weight: 0.9980 chunk 380 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 431 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN g 92 GLN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 441 GLN ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 42 GLN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN R 85 GLN T 111 HIS 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 405 GLN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 340 HIS a 76 ASN ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 610 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 68434 Z= 0.191 Angle : 0.627 16.664 92493 Z= 0.325 Chirality : 0.043 0.263 10483 Planarity : 0.004 0.075 11849 Dihedral : 4.485 32.547 9314 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.06 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.45 (0.09), residues: 8508 helix: 1.34 (0.07), residues: 4797 sheet: -0.40 (0.20), residues: 711 loop : -1.21 (0.12), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP f 21 HIS 0.006 0.001 HIS f 36 PHE 0.034 0.002 PHE 3 244 TYR 0.034 0.001 TYR g 144 ARG 0.017 0.000 ARG 0 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 922 time to evaluate : 6.108 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 19 MET cc_start: 0.9269 (tmm) cc_final: 0.8805 (ptp) REVERT: b 103 TYR cc_start: 0.8836 (m-10) cc_final: 0.8617 (m-10) REVERT: b 148 ASN cc_start: 0.8348 (t0) cc_final: 0.7955 (t0) REVERT: b 166 ASP cc_start: 0.8492 (t0) cc_final: 0.8210 (t0) REVERT: b 182 PHE cc_start: 0.9208 (m-80) cc_final: 0.8713 (m-80) REVERT: g 36 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8578 (mmmm) REVERT: g 47 MET cc_start: 0.9052 (mmm) cc_final: 0.8376 (mmp) REVERT: g 48 ARG cc_start: 0.9178 (mmp80) cc_final: 0.8955 (mmp80) REVERT: g 115 ASP cc_start: 0.6742 (t70) cc_final: 0.5523 (t0) REVERT: g 123 GLN cc_start: 0.8764 (mp10) cc_final: 0.8400 (mp10) REVERT: g 127 LEU cc_start: 0.9338 (mm) cc_final: 0.8705 (pp) REVERT: h 23 MET cc_start: 0.8908 (tpt) cc_final: 0.8454 (mtt) REVERT: h 53 MET cc_start: 0.5519 (ttt) cc_final: 0.5077 (tmm) REVERT: h 64 ILE cc_start: 0.9665 (mm) cc_final: 0.9458 (mm) REVERT: h 68 TYR cc_start: 0.9398 (m-10) cc_final: 0.9164 (m-10) REVERT: h 127 LEU cc_start: 0.8466 (mt) cc_final: 0.8087 (mt) REVERT: h 144 TYR cc_start: 0.9714 (m-80) cc_final: 0.9437 (m-80) REVERT: i 144 TYR cc_start: 0.8290 (m-10) cc_final: 0.7910 (m-10) REVERT: j 25 PHE cc_start: 0.8842 (m-10) cc_final: 0.8500 (m-80) REVERT: j 53 MET cc_start: 0.7547 (mmm) cc_final: 0.7009 (tpp) REVERT: j 67 ILE cc_start: 0.8580 (mm) cc_final: 0.8366 (mm) REVERT: j 140 VAL cc_start: 0.9286 (p) cc_final: 0.8845 (m) REVERT: k 53 MET cc_start: 0.6787 (ttt) cc_final: 0.6052 (tpp) REVERT: k 61 MET cc_start: 0.7821 (ppp) cc_final: 0.7427 (ppp) REVERT: k 131 MET cc_start: 0.9067 (ttp) cc_final: 0.8740 (tmm) REVERT: l 28 MET cc_start: 0.7483 (mmp) cc_final: 0.7209 (mmp) REVERT: l 53 MET cc_start: 0.6344 (tmm) cc_final: 0.5556 (tpt) REVERT: l 61 MET cc_start: 0.6862 (ptm) cc_final: 0.6598 (ptm) REVERT: l 147 ILE cc_start: 0.8740 (mm) cc_final: 0.8423 (mm) REVERT: m 61 MET cc_start: 0.8484 (mmt) cc_final: 0.8063 (mmt) REVERT: m 104 LEU cc_start: 0.9232 (mt) cc_final: 0.8876 (mt) REVERT: n 25 PHE cc_start: 0.9483 (m-80) cc_final: 0.9036 (m-10) REVERT: n 53 MET cc_start: 0.8361 (pmm) cc_final: 0.8056 (pmm) REVERT: n 54 LYS cc_start: 0.9628 (mmmt) cc_final: 0.9261 (mtpt) REVERT: n 78 ASN cc_start: 0.7584 (m-40) cc_final: 0.7173 (p0) REVERT: n 131 MET cc_start: 0.8316 (mmp) cc_final: 0.7631 (mmt) REVERT: o 28 MET cc_start: 0.8798 (mmp) cc_final: 0.8308 (mmm) REVERT: o 47 MET cc_start: 0.8417 (ttp) cc_final: 0.7896 (tmm) REVERT: o 68 TYR cc_start: 0.8688 (m-10) cc_final: 0.8194 (m-80) REVERT: o 144 TYR cc_start: 0.8838 (m-10) cc_final: 0.8602 (m-80) REVERT: 1 108 ASP cc_start: 0.9488 (m-30) cc_final: 0.9231 (m-30) REVERT: 1 277 CYS cc_start: 0.8652 (t) cc_final: 0.8048 (t) REVERT: 1 318 MET cc_start: 0.9497 (mmp) cc_final: 0.9175 (mmm) REVERT: 1 340 MET cc_start: 0.8728 (tpp) cc_final: 0.8497 (tpp) REVERT: 1 350 SER cc_start: 0.9097 (m) cc_final: 0.8749 (p) REVERT: 1 416 ASP cc_start: 0.8462 (t0) cc_final: 0.8205 (t70) REVERT: 1 461 LEU cc_start: 0.9420 (mt) cc_final: 0.9054 (pp) REVERT: 1 540 MET cc_start: 0.9233 (mtp) cc_final: 0.8784 (mtp) REVERT: 1 544 MET cc_start: 0.9407 (mpp) cc_final: 0.9121 (mpp) REVERT: 1 550 MET cc_start: 0.9637 (mtp) cc_final: 0.9061 (ttp) REVERT: 1 574 MET cc_start: 0.9000 (mtt) cc_final: 0.8639 (mmt) REVERT: 1 608 MET cc_start: 0.9326 (ptm) cc_final: 0.9071 (ppp) REVERT: 2 306 MET cc_start: 0.9477 (tmm) cc_final: 0.9232 (tmm) REVERT: 2 318 MET cc_start: 0.9423 (mmp) cc_final: 0.8942 (mmm) REVERT: 2 340 MET cc_start: 0.9047 (ttm) cc_final: 0.8560 (ttm) REVERT: 2 346 MET cc_start: 0.9218 (tpt) cc_final: 0.8778 (tpp) REVERT: 2 465 TYR cc_start: 0.9293 (m-80) cc_final: 0.9035 (m-80) REVERT: 2 540 MET cc_start: 0.8372 (mtm) cc_final: 0.7902 (mtp) REVERT: 2 550 MET cc_start: 0.9668 (tpt) cc_final: 0.9144 (tpp) REVERT: 2 574 MET cc_start: 0.8401 (mpp) cc_final: 0.7926 (mpp) REVERT: 2 584 MET cc_start: 0.8649 (ppp) cc_final: 0.8347 (ppp) REVERT: 3 127 MET cc_start: 0.9166 (tpp) cc_final: 0.8817 (tpp) REVERT: 3 231 PHE cc_start: 0.8991 (t80) cc_final: 0.8766 (t80) REVERT: 3 238 MET cc_start: 0.9207 (ppp) cc_final: 0.8897 (ppp) REVERT: 3 248 PHE cc_start: 0.9608 (m-10) cc_final: 0.9322 (m-80) REVERT: 3 309 GLU cc_start: 0.9587 (tm-30) cc_final: 0.9306 (tm-30) REVERT: 3 367 ASP cc_start: 0.8995 (m-30) cc_final: 0.8765 (m-30) REVERT: 3 402 MET cc_start: 0.8640 (mmt) cc_final: 0.8282 (mmt) REVERT: 3 435 MET cc_start: 0.9230 (mtm) cc_final: 0.9019 (ptp) REVERT: 3 449 LEU cc_start: 0.9746 (tp) cc_final: 0.9470 (pp) REVERT: 3 491 MET cc_start: 0.9502 (ptp) cc_final: 0.9242 (ptp) REVERT: 4 97 GLN cc_start: 0.9172 (pt0) cc_final: 0.8928 (pm20) REVERT: 4 180 MET cc_start: 0.9516 (tpp) cc_final: 0.9246 (tpp) REVERT: 4 187 GLN cc_start: 0.7794 (tt0) cc_final: 0.7479 (tm-30) REVERT: 4 234 MET cc_start: 0.8173 (tmm) cc_final: 0.7224 (tmm) REVERT: 4 279 LEU cc_start: 0.9894 (mm) cc_final: 0.9261 (mt) REVERT: 4 283 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8871 (mp0) REVERT: 4 299 ASP cc_start: 0.8799 (t0) cc_final: 0.8440 (t0) REVERT: 4 491 MET cc_start: 0.8595 (ptp) cc_final: 0.8388 (pmm) REVERT: 4 492 LEU cc_start: 0.9402 (mp) cc_final: 0.9120 (mp) REVERT: 5 214 LYS cc_start: 0.8733 (mttt) cc_final: 0.8255 (tppt) REVERT: 5 270 GLU cc_start: 0.8604 (tp30) cc_final: 0.8370 (tp30) REVERT: 5 283 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9195 (pt0) REVERT: 5 356 MET cc_start: 0.9303 (ttt) cc_final: 0.9059 (tpp) REVERT: 5 453 GLU cc_start: 0.9430 (tt0) cc_final: 0.9126 (tm-30) REVERT: 7 56 MET cc_start: 0.9066 (mmp) cc_final: 0.8684 (mmp) REVERT: 7 204 LYS cc_start: 0.9712 (mmmt) cc_final: 0.9330 (mmmt) REVERT: 8 132 MET cc_start: 0.7507 (mmp) cc_final: 0.6898 (mmm) REVERT: 8 207 MET cc_start: 0.8889 (mmm) cc_final: 0.8454 (mmm) REVERT: 9 124 LEU cc_start: 0.9650 (tp) cc_final: 0.9379 (pp) REVERT: 9 207 MET cc_start: 0.9345 (tpp) cc_final: 0.9105 (tpp) REVERT: X 44 THR cc_start: 0.9088 (p) cc_final: 0.8159 (t) REVERT: X 46 ASN cc_start: 0.9282 (p0) cc_final: 0.9037 (p0) REVERT: X 47 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9347 (pt0) REVERT: X 57 ASN cc_start: 0.9268 (m110) cc_final: 0.8970 (m110) REVERT: 6 23 HIS cc_start: 0.8671 (t-170) cc_final: 0.8394 (t-170) REVERT: 6 61 LEU cc_start: 0.7800 (tt) cc_final: 0.7260 (pp) REVERT: 6 134 ASN cc_start: 0.9381 (m-40) cc_final: 0.8974 (m110) REVERT: U 65 MET cc_start: 0.6357 (tpt) cc_final: 0.4410 (mtt) REVERT: U 239 LEU cc_start: 0.9185 (mt) cc_final: 0.8864 (tt) REVERT: U 289 PHE cc_start: 0.9190 (m-10) cc_final: 0.8859 (m-80) REVERT: d 44 ASP cc_start: 0.9558 (m-30) cc_final: 0.9254 (t0) REVERT: d 48 HIS cc_start: 0.8848 (m-70) cc_final: 0.8555 (m-70) REVERT: d 78 MET cc_start: 0.9049 (tpp) cc_final: 0.8595 (tpp) REVERT: d 171 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8522 (tm-30) REVERT: d 195 LYS cc_start: 0.9639 (ptmm) cc_final: 0.9371 (pttm) REVERT: d 297 HIS cc_start: 0.9406 (t70) cc_final: 0.9129 (t-90) REVERT: d 322 LYS cc_start: 0.9529 (tptm) cc_final: 0.9303 (tppt) REVERT: a 362 MET cc_start: 0.8132 (ppp) cc_final: 0.7263 (ppp) REVERT: a 382 GLN cc_start: 0.8594 (tp-100) cc_final: 0.7659 (tp-100) REVERT: a 430 MET cc_start: 0.8540 (mmp) cc_final: 0.8205 (mmm) REVERT: a 546 LYS cc_start: 0.8530 (mttt) cc_final: 0.8109 (mttt) REVERT: a 551 LEU cc_start: 0.9441 (mp) cc_final: 0.9238 (mp) REVERT: a 635 MET cc_start: 0.4348 (tmm) cc_final: 0.4145 (tmm) REVERT: a 747 SER cc_start: 0.8575 (t) cc_final: 0.8042 (m) REVERT: a 809 TRP cc_start: 0.8724 (t60) cc_final: 0.8271 (t60) REVERT: a 823 LYS cc_start: 0.9480 (tptp) cc_final: 0.9276 (tptt) REVERT: c 381 ASN cc_start: 0.8670 (t0) cc_final: 0.8371 (m110) REVERT: c 439 MET cc_start: 0.9578 (mmp) cc_final: 0.9126 (mmm) REVERT: 0 318 MET cc_start: 0.9430 (mmp) cc_final: 0.9148 (mmm) REVERT: 0 347 MET cc_start: 0.9191 (tpt) cc_final: 0.8986 (tpp) REVERT: 0 433 TRP cc_start: 0.8871 (t-100) cc_final: 0.8466 (t-100) REVERT: f 33 PHE cc_start: 0.9638 (m-80) cc_final: 0.9404 (m-80) REVERT: f 67 TYR cc_start: 0.8833 (m-80) cc_final: 0.8500 (t80) REVERT: f 70 PHE cc_start: 0.8939 (m-10) cc_final: 0.8733 (m-10) REVERT: s 141 MET cc_start: -0.4435 (tpp) cc_final: -0.4676 (tpp) REVERT: s 180 GLU cc_start: 0.9525 (tp30) cc_final: 0.9169 (tm-30) REVERT: s 181 MET cc_start: 0.6369 (tpp) cc_final: 0.6000 (tpp) REVERT: s 183 MET cc_start: 0.5548 (ptt) cc_final: 0.5015 (ptt) outliers start: 3 outliers final: 0 residues processed: 925 average time/residue: 0.6059 time to fit residues: 974.0732 Evaluate side-chains 725 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 725 time to evaluate : 6.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 468 optimal weight: 0.1980 chunk 600 optimal weight: 5.9990 chunk 465 optimal weight: 4.9990 chunk 692 optimal weight: 3.9990 chunk 459 optimal weight: 8.9990 chunk 819 optimal weight: 6.9990 chunk 512 optimal weight: 20.0000 chunk 499 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 171 GLN ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 152 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 280 ASN ** a 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 68434 Z= 0.248 Angle : 0.634 11.912 92493 Z= 0.336 Chirality : 0.042 0.275 10483 Planarity : 0.004 0.064 11849 Dihedral : 4.486 32.845 9314 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 0.01 % Allowed : 2.09 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 8508 helix: 1.30 (0.07), residues: 4808 sheet: -0.45 (0.20), residues: 730 loop : -1.22 (0.12), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 2 450 HIS 0.008 0.001 HIS a 555 PHE 0.029 0.002 PHE j 137 TYR 0.036 0.002 TYR 0 117 ARG 0.012 0.000 ARG 0 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 879 time to evaluate : 6.123 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: b 69 ILE cc_start: 0.9455 (mt) cc_final: 0.9241 (mt) REVERT: b 142 LEU cc_start: 0.9137 (tt) cc_final: 0.8816 (tt) REVERT: b 146 LEU cc_start: 0.8968 (mm) cc_final: 0.8718 (mm) REVERT: b 148 ASN cc_start: 0.8360 (t0) cc_final: 0.7937 (t0) REVERT: b 166 ASP cc_start: 0.8541 (t0) cc_final: 0.8285 (t0) REVERT: b 182 PHE cc_start: 0.9216 (m-80) cc_final: 0.8700 (m-80) REVERT: g 36 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8687 (mmmm) REVERT: g 47 MET cc_start: 0.9040 (mmm) cc_final: 0.8798 (mmp) REVERT: g 123 GLN cc_start: 0.8824 (mp10) cc_final: 0.8470 (mp10) REVERT: g 127 LEU cc_start: 0.9374 (mm) cc_final: 0.8738 (pp) REVERT: h 23 MET cc_start: 0.8944 (tpt) cc_final: 0.8511 (mtt) REVERT: h 53 MET cc_start: 0.5517 (ttt) cc_final: 0.5038 (tmm) REVERT: h 64 ILE cc_start: 0.9665 (mm) cc_final: 0.9453 (mm) REVERT: h 68 TYR cc_start: 0.9419 (m-10) cc_final: 0.9161 (m-10) REVERT: h 127 LEU cc_start: 0.8515 (mt) cc_final: 0.8163 (mt) REVERT: h 144 TYR cc_start: 0.9727 (m-80) cc_final: 0.9459 (m-80) REVERT: i 144 TYR cc_start: 0.8215 (m-10) cc_final: 0.7814 (m-10) REVERT: j 25 PHE cc_start: 0.8898 (m-10) cc_final: 0.8527 (m-80) REVERT: j 53 MET cc_start: 0.7568 (mmm) cc_final: 0.7028 (tpp) REVERT: j 67 ILE cc_start: 0.8630 (mm) cc_final: 0.8412 (mm) REVERT: j 140 VAL cc_start: 0.9359 (p) cc_final: 0.8924 (m) REVERT: k 53 MET cc_start: 0.6751 (ttt) cc_final: 0.6494 (ttt) REVERT: k 61 MET cc_start: 0.7697 (ppp) cc_final: 0.7244 (ppp) REVERT: k 131 MET cc_start: 0.9088 (ttp) cc_final: 0.8768 (tmm) REVERT: l 28 MET cc_start: 0.7434 (mmp) cc_final: 0.7184 (mmp) REVERT: l 53 MET cc_start: 0.6407 (tmm) cc_final: 0.5621 (tpt) REVERT: l 61 MET cc_start: 0.6978 (ptm) cc_final: 0.6750 (ptm) REVERT: m 61 MET cc_start: 0.8436 (mmt) cc_final: 0.7745 (tpp) REVERT: m 104 LEU cc_start: 0.9245 (mt) cc_final: 0.8883 (mt) REVERT: n 25 PHE cc_start: 0.9423 (m-80) cc_final: 0.9123 (m-10) REVERT: n 53 MET cc_start: 0.8374 (pmm) cc_final: 0.8082 (pmm) REVERT: n 54 LYS cc_start: 0.9615 (mmmt) cc_final: 0.9260 (mtpt) REVERT: n 78 ASN cc_start: 0.7641 (m-40) cc_final: 0.7429 (m-40) REVERT: n 131 MET cc_start: 0.8283 (mmp) cc_final: 0.7623 (mmt) REVERT: o 28 MET cc_start: 0.8843 (mmp) cc_final: 0.8476 (mmm) REVERT: o 47 MET cc_start: 0.8557 (ttp) cc_final: 0.8082 (tmm) REVERT: o 68 TYR cc_start: 0.8737 (m-10) cc_final: 0.8271 (m-80) REVERT: 1 34 MET cc_start: 0.8958 (mmp) cc_final: 0.8582 (mmm) REVERT: 1 108 ASP cc_start: 0.9495 (m-30) cc_final: 0.9242 (m-30) REVERT: 1 274 TYR cc_start: 0.9202 (t80) cc_final: 0.8952 (t80) REVERT: 1 277 CYS cc_start: 0.8765 (t) cc_final: 0.8482 (t) REVERT: 1 318 MET cc_start: 0.9502 (mmp) cc_final: 0.9177 (mmm) REVERT: 1 340 MET cc_start: 0.8818 (tpp) cc_final: 0.8545 (tpp) REVERT: 1 540 MET cc_start: 0.9256 (mtp) cc_final: 0.8735 (mtp) REVERT: 1 544 MET cc_start: 0.9392 (mpp) cc_final: 0.9134 (mpp) REVERT: 1 550 MET cc_start: 0.9632 (mtp) cc_final: 0.8970 (ttp) REVERT: 1 574 MET cc_start: 0.8983 (mtt) cc_final: 0.8720 (mmt) REVERT: 1 608 MET cc_start: 0.9318 (ptm) cc_final: 0.9004 (ppp) REVERT: 2 95 MET cc_start: 0.8252 (tpp) cc_final: 0.7886 (tpp) REVERT: 2 263 LEU cc_start: 0.9831 (tp) cc_final: 0.9593 (pp) REVERT: 2 306 MET cc_start: 0.9462 (tmm) cc_final: 0.9207 (tmm) REVERT: 2 318 MET cc_start: 0.9418 (mmp) cc_final: 0.8904 (mmm) REVERT: 2 340 MET cc_start: 0.9046 (ttm) cc_final: 0.8598 (ttm) REVERT: 2 346 MET cc_start: 0.9219 (tpt) cc_final: 0.8825 (tpp) REVERT: 2 382 LEU cc_start: 0.9713 (tp) cc_final: 0.9507 (tt) REVERT: 2 465 TYR cc_start: 0.9335 (m-80) cc_final: 0.9055 (m-80) REVERT: 2 544 MET cc_start: 0.9708 (mtp) cc_final: 0.9327 (mmt) REVERT: 2 550 MET cc_start: 0.9661 (tpt) cc_final: 0.9143 (tpp) REVERT: 2 574 MET cc_start: 0.8418 (mpp) cc_final: 0.7937 (mpp) REVERT: 3 238 MET cc_start: 0.9239 (ppp) cc_final: 0.8940 (ppp) REVERT: 3 248 PHE cc_start: 0.9620 (m-10) cc_final: 0.9318 (m-80) REVERT: 3 300 MET cc_start: 0.9522 (mmp) cc_final: 0.9103 (mmp) REVERT: 3 309 GLU cc_start: 0.9600 (tm-30) cc_final: 0.9321 (tm-30) REVERT: 3 367 ASP cc_start: 0.8909 (m-30) cc_final: 0.8694 (m-30) REVERT: 3 402 MET cc_start: 0.8739 (mmt) cc_final: 0.8401 (mmt) REVERT: 3 431 ASP cc_start: 0.9713 (t0) cc_final: 0.9285 (t0) REVERT: 3 435 MET cc_start: 0.9177 (mtm) cc_final: 0.8778 (ptp) REVERT: 3 449 LEU cc_start: 0.9748 (tp) cc_final: 0.9484 (pp) REVERT: 4 97 GLN cc_start: 0.9220 (pt0) cc_final: 0.8958 (pm20) REVERT: 4 180 MET cc_start: 0.9504 (tpp) cc_final: 0.9242 (tpp) REVERT: 4 187 GLN cc_start: 0.7869 (tt0) cc_final: 0.7495 (tm-30) REVERT: 4 234 MET cc_start: 0.8109 (tmm) cc_final: 0.7361 (tmm) REVERT: 4 279 LEU cc_start: 0.9892 (mm) cc_final: 0.9257 (mt) REVERT: 4 283 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8873 (mp0) REVERT: 4 299 ASP cc_start: 0.8837 (t0) cc_final: 0.8524 (t0) REVERT: 5 214 LYS cc_start: 0.8707 (mttt) cc_final: 0.8219 (tppt) REVERT: 5 270 GLU cc_start: 0.8689 (tp30) cc_final: 0.8482 (tp30) REVERT: 5 283 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9273 (mt-10) REVERT: 5 356 MET cc_start: 0.9287 (ttt) cc_final: 0.9010 (tpp) REVERT: 5 453 GLU cc_start: 0.9444 (tt0) cc_final: 0.9136 (tm-30) REVERT: 7 56 MET cc_start: 0.9095 (mmp) cc_final: 0.8700 (mmp) REVERT: 7 136 ARG cc_start: 0.9332 (ptp-170) cc_final: 0.8989 (ptt-90) REVERT: 7 204 LYS cc_start: 0.9704 (mmmt) cc_final: 0.9304 (mmmt) REVERT: 8 132 MET cc_start: 0.7492 (mmp) cc_final: 0.6874 (mmm) REVERT: 9 124 LEU cc_start: 0.9666 (tp) cc_final: 0.9382 (pp) REVERT: X 47 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9308 (pt0) REVERT: X 57 ASN cc_start: 0.9259 (m110) cc_final: 0.8929 (m-40) REVERT: 6 23 HIS cc_start: 0.8769 (t-170) cc_final: 0.8458 (t-170) REVERT: 6 134 ASN cc_start: 0.9393 (m-40) cc_final: 0.8994 (m110) REVERT: U 65 MET cc_start: 0.6259 (tpt) cc_final: 0.4257 (mtt) REVERT: U 239 LEU cc_start: 0.9230 (mt) cc_final: 0.8881 (tt) REVERT: U 289 PHE cc_start: 0.9165 (m-10) cc_final: 0.8783 (m-80) REVERT: d 44 ASP cc_start: 0.9551 (m-30) cc_final: 0.9256 (t0) REVERT: d 48 HIS cc_start: 0.8804 (m-70) cc_final: 0.8475 (m-70) REVERT: d 138 MET cc_start: 0.9324 (mpp) cc_final: 0.9060 (mpp) REVERT: d 171 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8502 (tm-30) REVERT: d 195 LYS cc_start: 0.9647 (ptmm) cc_final: 0.9388 (pttm) REVERT: d 297 HIS cc_start: 0.9422 (t70) cc_final: 0.9171 (t-90) REVERT: a 277 MET cc_start: 0.9367 (tmm) cc_final: 0.9012 (mmp) REVERT: a 362 MET cc_start: 0.8124 (ppp) cc_final: 0.7278 (ppp) REVERT: a 408 PHE cc_start: 0.8907 (p90) cc_final: 0.8630 (p90) REVERT: a 430 MET cc_start: 0.8529 (mmp) cc_final: 0.8197 (mmm) REVERT: a 460 MET cc_start: 0.9039 (mmp) cc_final: 0.8623 (mmm) REVERT: a 546 LYS cc_start: 0.8568 (mttt) cc_final: 0.8163 (mttp) REVERT: a 583 GLU cc_start: 0.9031 (mp0) cc_final: 0.8344 (pp20) REVERT: a 635 MET cc_start: 0.4450 (tmm) cc_final: 0.4205 (tmm) REVERT: a 658 MET cc_start: 0.6704 (mpp) cc_final: 0.5469 (mpp) REVERT: a 747 SER cc_start: 0.8565 (t) cc_final: 0.7935 (m) REVERT: a 809 TRP cc_start: 0.8745 (t60) cc_final: 0.8269 (t60) REVERT: c 439 MET cc_start: 0.9603 (mmp) cc_final: 0.9143 (mmm) REVERT: 0 39 MET cc_start: 0.8245 (tmm) cc_final: 0.8028 (tmm) REVERT: 0 108 ASP cc_start: 0.9344 (t70) cc_final: 0.9100 (t0) REVERT: 0 347 MET cc_start: 0.9210 (tpt) cc_final: 0.8943 (tpp) REVERT: 0 433 TRP cc_start: 0.8913 (t-100) cc_final: 0.8464 (t-100) REVERT: f 33 PHE cc_start: 0.9638 (m-80) cc_final: 0.9405 (m-80) REVERT: f 67 TYR cc_start: 0.8844 (m-80) cc_final: 0.8511 (t80) REVERT: s 141 MET cc_start: -0.4167 (tpp) cc_final: -0.4421 (tpp) REVERT: s 180 GLU cc_start: 0.9543 (tp30) cc_final: 0.9189 (tm-30) REVERT: s 181 MET cc_start: 0.6381 (tpp) cc_final: 0.6027 (tpp) REVERT: s 183 MET cc_start: 0.5645 (ptt) cc_final: 0.5085 (ptt) outliers start: 1 outliers final: 0 residues processed: 880 average time/residue: 0.5970 time to fit residues: 911.9740 Evaluate side-chains 704 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 6.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 8.9990 chunk 327 optimal weight: 5.9990 chunk 489 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 520 optimal weight: 10.0000 chunk 558 optimal weight: 9.9990 chunk 405 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 643 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 199 HIS ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 152 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 GLN ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 ASN ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 68434 Z= 0.183 Angle : 0.635 12.409 92493 Z= 0.329 Chirality : 0.043 0.288 10483 Planarity : 0.004 0.061 11849 Dihedral : 4.432 34.942 9314 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 0.01 % Allowed : 1.34 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.46 (0.09), residues: 8508 helix: 1.35 (0.07), residues: 4803 sheet: -0.40 (0.20), residues: 746 loop : -1.22 (0.12), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 2 450 HIS 0.005 0.001 HIS R 111 PHE 0.029 0.002 PHE s 150 TYR 0.045 0.001 TYR m 144 ARG 0.009 0.000 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 899 time to evaluate : 6.164 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: b 19 MET cc_start: 0.9329 (tmm) cc_final: 0.8775 (ptm) REVERT: b 103 TYR cc_start: 0.8848 (m-10) cc_final: 0.8506 (m-10) REVERT: b 148 ASN cc_start: 0.8314 (t0) cc_final: 0.8007 (t0) REVERT: b 166 ASP cc_start: 0.8487 (t0) cc_final: 0.8222 (t0) REVERT: b 182 PHE cc_start: 0.9265 (m-80) cc_final: 0.8691 (m-80) REVERT: g 25 PHE cc_start: 0.9081 (m-80) cc_final: 0.8838 (m-80) REVERT: g 36 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8866 (mmmm) REVERT: g 47 MET cc_start: 0.9035 (mmm) cc_final: 0.8805 (mmp) REVERT: g 123 GLN cc_start: 0.8776 (mp10) cc_final: 0.8500 (mp10) REVERT: g 127 LEU cc_start: 0.9324 (mm) cc_final: 0.8782 (pp) REVERT: h 23 MET cc_start: 0.8902 (tpt) cc_final: 0.8469 (mtt) REVERT: h 53 MET cc_start: 0.5434 (ttt) cc_final: 0.4938 (tmm) REVERT: h 64 ILE cc_start: 0.9650 (mm) cc_final: 0.9424 (mm) REVERT: h 68 TYR cc_start: 0.9407 (m-10) cc_final: 0.9153 (m-10) REVERT: h 127 LEU cc_start: 0.8440 (mt) cc_final: 0.8080 (mt) REVERT: h 144 TYR cc_start: 0.9726 (m-80) cc_final: 0.9443 (m-80) REVERT: i 144 TYR cc_start: 0.8269 (m-10) cc_final: 0.7866 (m-10) REVERT: j 25 PHE cc_start: 0.8864 (m-10) cc_final: 0.8610 (m-10) REVERT: j 64 ILE cc_start: 0.8708 (tp) cc_final: 0.8485 (tp) REVERT: j 67 ILE cc_start: 0.8602 (mm) cc_final: 0.8388 (mm) REVERT: j 140 VAL cc_start: 0.9335 (p) cc_final: 0.8887 (m) REVERT: k 53 MET cc_start: 0.6685 (ttt) cc_final: 0.6423 (ttt) REVERT: k 61 MET cc_start: 0.7802 (ppp) cc_final: 0.7370 (ppp) REVERT: k 131 MET cc_start: 0.9089 (ttp) cc_final: 0.8813 (ppp) REVERT: l 28 MET cc_start: 0.7279 (mmp) cc_final: 0.7058 (mmp) REVERT: l 53 MET cc_start: 0.6281 (tmm) cc_final: 0.5548 (tpt) REVERT: l 61 MET cc_start: 0.7124 (ptm) cc_final: 0.6807 (ptm) REVERT: l 147 ILE cc_start: 0.8723 (mm) cc_final: 0.8445 (mm) REVERT: m 61 MET cc_start: 0.8604 (mmt) cc_final: 0.8073 (tpp) REVERT: m 104 LEU cc_start: 0.9239 (mt) cc_final: 0.8891 (mt) REVERT: n 25 PHE cc_start: 0.9468 (m-80) cc_final: 0.9017 (m-10) REVERT: n 53 MET cc_start: 0.8340 (pmm) cc_final: 0.8052 (pmm) REVERT: n 54 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9256 (mtpt) REVERT: n 131 MET cc_start: 0.8245 (mmp) cc_final: 0.7653 (mmt) REVERT: o 28 MET cc_start: 0.8912 (mmp) cc_final: 0.8421 (mmm) REVERT: o 47 MET cc_start: 0.8439 (ttp) cc_final: 0.7930 (tmm) REVERT: o 68 TYR cc_start: 0.8564 (m-10) cc_final: 0.8092 (m-80) REVERT: 1 34 MET cc_start: 0.9156 (mmp) cc_final: 0.8722 (mmm) REVERT: 1 108 ASP cc_start: 0.9474 (m-30) cc_final: 0.9207 (m-30) REVERT: 1 274 TYR cc_start: 0.9178 (t80) cc_final: 0.8971 (t80) REVERT: 1 277 CYS cc_start: 0.8722 (t) cc_final: 0.8450 (t) REVERT: 1 318 MET cc_start: 0.9481 (mmp) cc_final: 0.9161 (mmm) REVERT: 1 340 MET cc_start: 0.8843 (tpp) cc_final: 0.8547 (tpp) REVERT: 1 461 LEU cc_start: 0.9444 (mt) cc_final: 0.9053 (pp) REVERT: 1 540 MET cc_start: 0.9239 (mtp) cc_final: 0.8661 (mtp) REVERT: 1 544 MET cc_start: 0.9377 (mpp) cc_final: 0.9111 (mpp) REVERT: 1 550 MET cc_start: 0.9662 (mtp) cc_final: 0.9007 (ttp) REVERT: 1 574 MET cc_start: 0.8949 (mtt) cc_final: 0.8592 (mmt) REVERT: 1 608 MET cc_start: 0.9338 (ptm) cc_final: 0.9020 (ppp) REVERT: 2 95 MET cc_start: 0.8294 (tpp) cc_final: 0.7855 (tpp) REVERT: 2 263 LEU cc_start: 0.9827 (tp) cc_final: 0.9583 (pp) REVERT: 2 306 MET cc_start: 0.9484 (tmm) cc_final: 0.9190 (tmm) REVERT: 2 318 MET cc_start: 0.9380 (mmp) cc_final: 0.8918 (mmm) REVERT: 2 340 MET cc_start: 0.9063 (ttm) cc_final: 0.8584 (ttm) REVERT: 2 346 MET cc_start: 0.9225 (tpt) cc_final: 0.8793 (tpp) REVERT: 2 382 LEU cc_start: 0.9707 (tp) cc_final: 0.9486 (tt) REVERT: 2 465 TYR cc_start: 0.9321 (m-80) cc_final: 0.9085 (m-80) REVERT: 2 540 MET cc_start: 0.8351 (mtm) cc_final: 0.7853 (mtp) REVERT: 2 550 MET cc_start: 0.9659 (tpt) cc_final: 0.9138 (tpp) REVERT: 2 574 MET cc_start: 0.8419 (mpp) cc_final: 0.7903 (mpp) REVERT: 2 584 MET cc_start: 0.8692 (ppp) cc_final: 0.8366 (ppp) REVERT: 3 180 MET cc_start: 0.9035 (mmp) cc_final: 0.8808 (mmm) REVERT: 3 231 PHE cc_start: 0.8905 (t80) cc_final: 0.8463 (t80) REVERT: 3 238 MET cc_start: 0.9198 (ppp) cc_final: 0.8871 (ppp) REVERT: 3 248 PHE cc_start: 0.9482 (m-10) cc_final: 0.9178 (m-80) REVERT: 3 300 MET cc_start: 0.9520 (mmp) cc_final: 0.9083 (mmp) REVERT: 3 309 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9297 (tm-30) REVERT: 3 367 ASP cc_start: 0.8955 (m-30) cc_final: 0.8724 (m-30) REVERT: 3 402 MET cc_start: 0.8717 (mmt) cc_final: 0.8330 (mmp) REVERT: 3 431 ASP cc_start: 0.9707 (t0) cc_final: 0.9430 (t0) REVERT: 3 449 LEU cc_start: 0.9743 (tp) cc_final: 0.9474 (pp) REVERT: 3 491 MET cc_start: 0.9510 (ptp) cc_final: 0.9284 (ptp) REVERT: 4 97 GLN cc_start: 0.9175 (pt0) cc_final: 0.8944 (pm20) REVERT: 4 180 MET cc_start: 0.9523 (tpp) cc_final: 0.9270 (tpp) REVERT: 4 187 GLN cc_start: 0.7765 (tt0) cc_final: 0.6879 (tm-30) REVERT: 4 234 MET cc_start: 0.8220 (tmm) cc_final: 0.7595 (tmm) REVERT: 4 279 LEU cc_start: 0.9891 (mm) cc_final: 0.9251 (mt) REVERT: 4 283 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8859 (mp0) REVERT: 4 299 ASP cc_start: 0.8743 (t0) cc_final: 0.8441 (t0) REVERT: 4 492 LEU cc_start: 0.9377 (mp) cc_final: 0.9171 (mp) REVERT: 5 214 LYS cc_start: 0.8695 (mttt) cc_final: 0.8300 (mtmt) REVERT: 5 270 GLU cc_start: 0.8652 (tp30) cc_final: 0.8427 (tp30) REVERT: 5 283 GLU cc_start: 0.9512 (mt-10) cc_final: 0.9224 (pt0) REVERT: 5 356 MET cc_start: 0.9304 (ttt) cc_final: 0.9058 (tpp) REVERT: 5 453 GLU cc_start: 0.9423 (tt0) cc_final: 0.9114 (tm-30) REVERT: 7 56 MET cc_start: 0.9076 (mmp) cc_final: 0.8692 (mmp) REVERT: 7 204 LYS cc_start: 0.9712 (mmmt) cc_final: 0.9308 (mmmt) REVERT: 8 38 PHE cc_start: 0.9512 (t80) cc_final: 0.9020 (t80) REVERT: 8 132 MET cc_start: 0.7431 (mmp) cc_final: 0.6800 (mmm) REVERT: 8 207 MET cc_start: 0.8965 (mmm) cc_final: 0.8473 (mmm) REVERT: 9 72 MET cc_start: 0.9374 (tmm) cc_final: 0.8994 (tmm) REVERT: 9 76 MET cc_start: 0.9327 (mmp) cc_final: 0.9125 (mmp) REVERT: 9 124 LEU cc_start: 0.9642 (tp) cc_final: 0.9374 (pp) REVERT: T 102 MET cc_start: 0.9549 (mmm) cc_final: 0.9021 (mmm) REVERT: X 47 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9326 (pt0) REVERT: X 57 ASN cc_start: 0.9253 (m110) cc_final: 0.8944 (m110) REVERT: 6 23 HIS cc_start: 0.8630 (t-170) cc_final: 0.8328 (t-170) REVERT: 6 61 LEU cc_start: 0.7880 (tt) cc_final: 0.7262 (pp) REVERT: 6 134 ASN cc_start: 0.9386 (m-40) cc_final: 0.8987 (m110) REVERT: U 65 MET cc_start: 0.6221 (tpt) cc_final: 0.4351 (mtt) REVERT: U 239 LEU cc_start: 0.9199 (mt) cc_final: 0.8863 (tt) REVERT: U 256 MET cc_start: 0.8766 (mpp) cc_final: 0.8521 (mmt) REVERT: U 289 PHE cc_start: 0.9143 (m-10) cc_final: 0.8797 (m-80) REVERT: d 44 ASP cc_start: 0.9549 (m-30) cc_final: 0.9244 (t0) REVERT: d 48 HIS cc_start: 0.8808 (m-70) cc_final: 0.8482 (m-70) REVERT: d 138 MET cc_start: 0.9340 (mpp) cc_final: 0.9083 (mpp) REVERT: d 195 LYS cc_start: 0.9646 (ptmm) cc_final: 0.9398 (pttm) REVERT: d 297 HIS cc_start: 0.9373 (t70) cc_final: 0.9007 (t70) REVERT: d 322 LYS cc_start: 0.9673 (tptm) cc_final: 0.9318 (tppt) REVERT: a 362 MET cc_start: 0.8150 (ppp) cc_final: 0.7304 (ppp) REVERT: a 382 GLN cc_start: 0.8572 (tp-100) cc_final: 0.7631 (tp-100) REVERT: a 408 PHE cc_start: 0.8919 (p90) cc_final: 0.8695 (p90) REVERT: a 413 MET cc_start: 0.7233 (tpp) cc_final: 0.7014 (tpp) REVERT: a 430 MET cc_start: 0.8529 (mmp) cc_final: 0.8182 (mmm) REVERT: a 460 MET cc_start: 0.9024 (mmp) cc_final: 0.8679 (mmm) REVERT: a 546 LYS cc_start: 0.8480 (mttt) cc_final: 0.8080 (mttp) REVERT: a 583 GLU cc_start: 0.9000 (mp0) cc_final: 0.8359 (pp20) REVERT: a 635 MET cc_start: 0.4312 (tmm) cc_final: 0.4039 (tmm) REVERT: a 658 MET cc_start: 0.6679 (mpp) cc_final: 0.5473 (mpp) REVERT: a 747 SER cc_start: 0.8488 (t) cc_final: 0.7956 (m) REVERT: a 809 TRP cc_start: 0.8735 (t60) cc_final: 0.8305 (t60) REVERT: c 439 MET cc_start: 0.9604 (mmp) cc_final: 0.9134 (mmm) REVERT: 0 39 MET cc_start: 0.8267 (tmm) cc_final: 0.7997 (tmm) REVERT: 0 108 ASP cc_start: 0.9329 (t70) cc_final: 0.9079 (t0) REVERT: 0 318 MET cc_start: 0.9438 (mmp) cc_final: 0.9009 (mmt) REVERT: 0 347 MET cc_start: 0.9183 (tpt) cc_final: 0.8913 (tpp) REVERT: 0 433 TRP cc_start: 0.8886 (t-100) cc_final: 0.8463 (t-100) REVERT: f 52 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8989 (mp0) REVERT: f 67 TYR cc_start: 0.8801 (m-80) cc_final: 0.8367 (t80) REVERT: f 70 PHE cc_start: 0.9154 (m-80) cc_final: 0.8657 (m-10) REVERT: s 153 MET cc_start: 0.6010 (tmm) cc_final: 0.5562 (tmm) REVERT: s 180 GLU cc_start: 0.9539 (tp30) cc_final: 0.9182 (tm-30) REVERT: s 181 MET cc_start: 0.6409 (tpp) cc_final: 0.6035 (tpp) REVERT: s 183 MET cc_start: 0.5634 (ptt) cc_final: 0.5089 (ptt) outliers start: 1 outliers final: 0 residues processed: 900 average time/residue: 0.6003 time to fit residues: 932.9655 Evaluate side-chains 707 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 30.0000 chunk 784 optimal weight: 3.9990 chunk 716 optimal weight: 0.8980 chunk 763 optimal weight: 8.9990 chunk 459 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 599 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 689 optimal weight: 9.9990 chunk 722 optimal weight: 1.9990 chunk 760 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN 6 194 HIS 6 322 GLN ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 767 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 68434 Z= 0.245 Angle : 0.650 11.430 92493 Z= 0.341 Chirality : 0.043 0.296 10483 Planarity : 0.004 0.060 11849 Dihedral : 4.490 36.752 9314 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.40 (0.09), residues: 8508 helix: 1.29 (0.07), residues: 4799 sheet: -0.42 (0.20), residues: 743 loop : -1.22 (0.12), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP f 21 HIS 0.007 0.001 HIS R 111 PHE 0.037 0.002 PHE T 55 TYR 0.035 0.001 TYR g 144 ARG 0.010 0.001 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 864 time to evaluate : 6.230 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 19 MET cc_start: 0.9301 (tmm) cc_final: 0.8728 (ptm) REVERT: b 69 ILE cc_start: 0.9451 (mt) cc_final: 0.9245 (mt) REVERT: b 142 LEU cc_start: 0.9120 (tt) cc_final: 0.8784 (tt) REVERT: b 146 LEU cc_start: 0.8966 (mm) cc_final: 0.8724 (mm) REVERT: b 148 ASN cc_start: 0.8360 (t0) cc_final: 0.8004 (t0) REVERT: b 166 ASP cc_start: 0.8531 (t0) cc_final: 0.8299 (t0) REVERT: b 182 PHE cc_start: 0.9290 (m-80) cc_final: 0.8754 (m-80) REVERT: g 25 PHE cc_start: 0.9119 (m-80) cc_final: 0.8872 (m-80) REVERT: g 36 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8661 (mmmm) REVERT: g 47 MET cc_start: 0.9025 (mmm) cc_final: 0.8807 (mmp) REVERT: g 123 GLN cc_start: 0.8780 (mp10) cc_final: 0.8449 (mp10) REVERT: g 127 LEU cc_start: 0.9370 (mm) cc_final: 0.8659 (pp) REVERT: h 23 MET cc_start: 0.8926 (tpt) cc_final: 0.8498 (mtt) REVERT: h 53 MET cc_start: 0.5334 (ttt) cc_final: 0.4876 (tmm) REVERT: h 64 ILE cc_start: 0.9667 (mm) cc_final: 0.9425 (mm) REVERT: h 68 TYR cc_start: 0.9412 (m-10) cc_final: 0.9151 (m-10) REVERT: h 127 LEU cc_start: 0.8558 (mt) cc_final: 0.8220 (mt) REVERT: h 144 TYR cc_start: 0.9727 (m-80) cc_final: 0.9453 (m-80) REVERT: i 17 MET cc_start: 0.9133 (mpp) cc_final: 0.8894 (mpp) REVERT: i 144 TYR cc_start: 0.8210 (m-10) cc_final: 0.7786 (m-10) REVERT: j 25 PHE cc_start: 0.8886 (m-10) cc_final: 0.8506 (m-80) REVERT: j 64 ILE cc_start: 0.8763 (tp) cc_final: 0.8546 (tp) REVERT: j 67 ILE cc_start: 0.8592 (mm) cc_final: 0.8391 (mm) REVERT: j 92 GLN cc_start: 0.8007 (mp10) cc_final: 0.7754 (mm110) REVERT: j 140 VAL cc_start: 0.9317 (p) cc_final: 0.8870 (m) REVERT: k 53 MET cc_start: 0.6633 (ttt) cc_final: 0.6416 (ttt) REVERT: k 61 MET cc_start: 0.7622 (ppp) cc_final: 0.7168 (ppp) REVERT: k 131 MET cc_start: 0.9068 (ttp) cc_final: 0.8835 (ppp) REVERT: l 28 MET cc_start: 0.7302 (mmp) cc_final: 0.7070 (mmp) REVERT: l 53 MET cc_start: 0.6325 (tmm) cc_final: 0.5561 (tpt) REVERT: l 147 ILE cc_start: 0.8708 (mm) cc_final: 0.8434 (mm) REVERT: m 61 MET cc_start: 0.8708 (mmt) cc_final: 0.8216 (tpp) REVERT: m 104 LEU cc_start: 0.9245 (mt) cc_final: 0.8886 (mt) REVERT: n 25 PHE cc_start: 0.9395 (m-80) cc_final: 0.9130 (m-10) REVERT: n 53 MET cc_start: 0.8357 (pmm) cc_final: 0.8046 (pmm) REVERT: n 54 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9273 (mtpt) REVERT: n 78 ASN cc_start: 0.7260 (m110) cc_final: 0.6869 (p0) REVERT: n 131 MET cc_start: 0.8291 (mmp) cc_final: 0.7605 (mmt) REVERT: o 28 MET cc_start: 0.8878 (mmp) cc_final: 0.8362 (mmm) REVERT: o 47 MET cc_start: 0.8643 (ttp) cc_final: 0.8068 (tmm) REVERT: o 68 TYR cc_start: 0.8622 (m-10) cc_final: 0.8138 (m-80) REVERT: 1 34 MET cc_start: 0.9159 (mmp) cc_final: 0.8762 (mmm) REVERT: 1 108 ASP cc_start: 0.9487 (m-30) cc_final: 0.9228 (m-30) REVERT: 1 274 TYR cc_start: 0.9220 (t80) cc_final: 0.8952 (t80) REVERT: 1 277 CYS cc_start: 0.8831 (t) cc_final: 0.8558 (t) REVERT: 1 318 MET cc_start: 0.9494 (mmp) cc_final: 0.9173 (mmm) REVERT: 1 340 MET cc_start: 0.8856 (tpp) cc_final: 0.8536 (tpp) REVERT: 1 461 LEU cc_start: 0.9488 (mt) cc_final: 0.9076 (pp) REVERT: 1 540 MET cc_start: 0.9228 (mtp) cc_final: 0.9021 (mtp) REVERT: 1 550 MET cc_start: 0.9654 (mtp) cc_final: 0.8978 (ttp) REVERT: 1 574 MET cc_start: 0.9015 (mtt) cc_final: 0.8717 (mmt) REVERT: 1 608 MET cc_start: 0.9302 (ptm) cc_final: 0.8993 (ppp) REVERT: 2 263 LEU cc_start: 0.9827 (tp) cc_final: 0.9583 (pp) REVERT: 2 318 MET cc_start: 0.9392 (mmp) cc_final: 0.8903 (mmm) REVERT: 2 340 MET cc_start: 0.9085 (ttm) cc_final: 0.8643 (ttm) REVERT: 2 346 MET cc_start: 0.9227 (tpt) cc_final: 0.8846 (tpp) REVERT: 2 382 LEU cc_start: 0.9705 (tp) cc_final: 0.9504 (tt) REVERT: 2 465 TYR cc_start: 0.9365 (m-80) cc_final: 0.9116 (m-80) REVERT: 2 544 MET cc_start: 0.9656 (mtp) cc_final: 0.9231 (mmt) REVERT: 2 550 MET cc_start: 0.9663 (tpt) cc_final: 0.9136 (tpp) REVERT: 2 574 MET cc_start: 0.8474 (mpp) cc_final: 0.7992 (mpp) REVERT: 2 584 MET cc_start: 0.8715 (ppp) cc_final: 0.8497 (ppp) REVERT: 3 231 PHE cc_start: 0.9074 (t80) cc_final: 0.8553 (t80) REVERT: 3 238 MET cc_start: 0.9214 (ppp) cc_final: 0.8943 (ppp) REVERT: 3 248 PHE cc_start: 0.9517 (m-10) cc_final: 0.9195 (m-80) REVERT: 3 309 GLU cc_start: 0.9608 (tm-30) cc_final: 0.9321 (tm-30) REVERT: 3 356 MET cc_start: 0.7877 (tpt) cc_final: 0.7646 (tpt) REVERT: 3 367 ASP cc_start: 0.8940 (m-30) cc_final: 0.8654 (m-30) REVERT: 3 402 MET cc_start: 0.8742 (mmt) cc_final: 0.8349 (mmt) REVERT: 3 431 ASP cc_start: 0.9720 (t0) cc_final: 0.9281 (t0) REVERT: 3 435 MET cc_start: 0.9182 (mtm) cc_final: 0.8725 (ptp) REVERT: 3 449 LEU cc_start: 0.9750 (tp) cc_final: 0.9484 (pp) REVERT: 3 491 MET cc_start: 0.9525 (ptp) cc_final: 0.9283 (ptp) REVERT: 4 97 GLN cc_start: 0.9231 (pt0) cc_final: 0.8973 (pm20) REVERT: 4 180 MET cc_start: 0.9412 (tpp) cc_final: 0.9210 (tpp) REVERT: 4 187 GLN cc_start: 0.7759 (tt0) cc_final: 0.7442 (tm-30) REVERT: 4 234 MET cc_start: 0.8102 (tmm) cc_final: 0.7316 (tmm) REVERT: 4 279 LEU cc_start: 0.9896 (mm) cc_final: 0.9466 (mt) REVERT: 4 283 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8874 (mt-10) REVERT: 4 299 ASP cc_start: 0.8792 (t0) cc_final: 0.8460 (t0) REVERT: 4 356 MET cc_start: 0.8774 (mtm) cc_final: 0.8375 (mpp) REVERT: 4 491 MET cc_start: 0.8514 (ptp) cc_final: 0.8230 (pmm) REVERT: 4 492 LEU cc_start: 0.9381 (mp) cc_final: 0.9098 (mp) REVERT: 5 214 LYS cc_start: 0.8677 (mttt) cc_final: 0.8188 (tppt) REVERT: 5 283 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9221 (mt-10) REVERT: 5 356 MET cc_start: 0.9293 (ttt) cc_final: 0.9043 (tpp) REVERT: 5 453 GLU cc_start: 0.9439 (tt0) cc_final: 0.9094 (tm-30) REVERT: 7 14 MET cc_start: 0.8961 (mmt) cc_final: 0.8760 (mmt) REVERT: 7 56 MET cc_start: 0.9101 (mmp) cc_final: 0.8705 (mmp) REVERT: 8 38 PHE cc_start: 0.9519 (t80) cc_final: 0.9033 (t80) REVERT: 8 132 MET cc_start: 0.7469 (mmp) cc_final: 0.6810 (mmm) REVERT: 8 207 MET cc_start: 0.8993 (mmm) cc_final: 0.8745 (mmm) REVERT: 9 72 MET cc_start: 0.9373 (tmm) cc_final: 0.8885 (tmm) REVERT: 9 76 MET cc_start: 0.9354 (mmp) cc_final: 0.9069 (mmp) REVERT: 9 124 LEU cc_start: 0.9628 (tp) cc_final: 0.9377 (pp) REVERT: R 63 MET cc_start: 0.6700 (pmm) cc_final: 0.6494 (pmm) REVERT: T 102 MET cc_start: 0.9542 (mmm) cc_final: 0.8953 (tpt) REVERT: V 49 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8174 (mtt-85) REVERT: X 37 LEU cc_start: 0.9732 (tp) cc_final: 0.9481 (tp) REVERT: X 47 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9314 (pt0) REVERT: X 57 ASN cc_start: 0.9275 (m110) cc_final: 0.8953 (m-40) REVERT: 6 23 HIS cc_start: 0.8707 (t-170) cc_final: 0.8342 (t-170) REVERT: 6 61 LEU cc_start: 0.7902 (tt) cc_final: 0.7511 (tp) REVERT: 6 134 ASN cc_start: 0.9382 (m-40) cc_final: 0.8985 (m110) REVERT: U 65 MET cc_start: 0.6117 (tpt) cc_final: 0.4115 (mtt) REVERT: U 239 LEU cc_start: 0.9229 (mt) cc_final: 0.8874 (tt) REVERT: U 289 PHE cc_start: 0.9194 (m-10) cc_final: 0.8809 (m-80) REVERT: d 44 ASP cc_start: 0.9547 (m-30) cc_final: 0.9252 (t0) REVERT: d 48 HIS cc_start: 0.8797 (m-70) cc_final: 0.8454 (m-70) REVERT: d 78 MET cc_start: 0.9009 (tpp) cc_final: 0.8771 (tpt) REVERT: d 138 MET cc_start: 0.9326 (mpp) cc_final: 0.9096 (mpp) REVERT: d 297 HIS cc_start: 0.9419 (t70) cc_final: 0.9097 (t70) REVERT: d 322 LYS cc_start: 0.9675 (tptm) cc_final: 0.9354 (tppt) REVERT: a 10 MET cc_start: 0.7981 (pmm) cc_final: 0.7537 (pmm) REVERT: a 277 MET cc_start: 0.9317 (tmm) cc_final: 0.8943 (mmp) REVERT: a 362 MET cc_start: 0.8129 (ppp) cc_final: 0.7311 (ppp) REVERT: a 408 PHE cc_start: 0.8915 (p90) cc_final: 0.8671 (p90) REVERT: a 413 MET cc_start: 0.7315 (tpp) cc_final: 0.7051 (tpp) REVERT: a 430 MET cc_start: 0.8550 (mmp) cc_final: 0.8216 (mmm) REVERT: a 460 MET cc_start: 0.9068 (mmp) cc_final: 0.8782 (mmm) REVERT: a 546 LYS cc_start: 0.8573 (mttt) cc_final: 0.8160 (mttt) REVERT: a 747 SER cc_start: 0.8547 (t) cc_final: 0.8044 (m) REVERT: a 795 MET cc_start: 0.9338 (mpp) cc_final: 0.8909 (mpp) REVERT: a 809 TRP cc_start: 0.8727 (t60) cc_final: 0.8261 (t60) REVERT: c 439 MET cc_start: 0.9598 (mmp) cc_final: 0.9156 (mmm) REVERT: 0 39 MET cc_start: 0.8341 (tmm) cc_final: 0.8037 (tmm) REVERT: 0 108 ASP cc_start: 0.9366 (t70) cc_final: 0.9142 (t0) REVERT: 0 340 MET cc_start: 0.8771 (tpp) cc_final: 0.8000 (tpp) REVERT: 0 347 MET cc_start: 0.9189 (tpt) cc_final: 0.8906 (tpp) REVERT: 0 433 TRP cc_start: 0.8983 (t-100) cc_final: 0.8497 (t-100) REVERT: 0 540 MET cc_start: 0.8588 (pmm) cc_final: 0.8367 (pmm) REVERT: f 52 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9022 (mp0) REVERT: f 67 TYR cc_start: 0.8824 (m-80) cc_final: 0.8404 (t80) REVERT: f 70 PHE cc_start: 0.9156 (m-80) cc_final: 0.8694 (m-10) REVERT: s 180 GLU cc_start: 0.9540 (tp30) cc_final: 0.9191 (tm-30) REVERT: s 181 MET cc_start: 0.6440 (tpp) cc_final: 0.6081 (tpp) REVERT: s 183 MET cc_start: 0.5722 (ptt) cc_final: 0.5123 (ptt) outliers start: 0 outliers final: 0 residues processed: 864 average time/residue: 0.6057 time to fit residues: 911.2878 Evaluate side-chains 692 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 5.9990 chunk 807 optimal weight: 10.0000 chunk 492 optimal weight: 0.6980 chunk 382 optimal weight: 0.9990 chunk 561 optimal weight: 30.0000 chunk 846 optimal weight: 7.9990 chunk 779 optimal weight: 0.9990 chunk 674 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 520 optimal weight: 5.9990 chunk 413 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 292 HIS ** 5 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 219 ASN 9 221 ASN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 ASN a 555 HIS ** a 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 622 ASN a 767 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 68434 Z= 0.211 Angle : 0.650 11.896 92493 Z= 0.337 Chirality : 0.043 0.302 10483 Planarity : 0.004 0.061 11849 Dihedral : 4.483 38.127 9314 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 0.01 % Allowed : 0.42 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 8508 helix: 1.30 (0.07), residues: 4794 sheet: -0.32 (0.20), residues: 736 loop : -1.26 (0.12), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP f 21 HIS 0.009 0.001 HIS a 555 PHE 0.030 0.002 PHE f 33 TYR 0.036 0.001 TYR g 144 ARG 0.007 0.000 ARG 0 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17016 Ramachandran restraints generated. 8508 Oldfield, 0 Emsley, 8508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 871 time to evaluate : 5.981 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: b 19 MET cc_start: 0.9292 (tmm) cc_final: 0.8734 (ptm) REVERT: b 69 ILE cc_start: 0.9437 (mt) cc_final: 0.9229 (mt) REVERT: b 103 TYR cc_start: 0.8856 (m-10) cc_final: 0.8613 (m-10) REVERT: b 148 ASN cc_start: 0.8243 (t0) cc_final: 0.7953 (t0) REVERT: b 166 ASP cc_start: 0.8503 (t0) cc_final: 0.8255 (t0) REVERT: b 182 PHE cc_start: 0.9289 (m-80) cc_final: 0.8762 (m-80) REVERT: g 25 PHE cc_start: 0.9106 (m-80) cc_final: 0.8870 (m-80) REVERT: g 36 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8653 (mmmm) REVERT: g 123 GLN cc_start: 0.8800 (mp10) cc_final: 0.8465 (mp10) REVERT: g 127 LEU cc_start: 0.9335 (mm) cc_final: 0.8657 (pp) REVERT: h 23 MET cc_start: 0.8915 (tpt) cc_final: 0.8487 (mtt) REVERT: h 53 MET cc_start: 0.5341 (ttt) cc_final: 0.4845 (tmm) REVERT: h 64 ILE cc_start: 0.9663 (mm) cc_final: 0.9417 (mm) REVERT: h 68 TYR cc_start: 0.9405 (m-10) cc_final: 0.9144 (m-10) REVERT: h 127 LEU cc_start: 0.8582 (mt) cc_final: 0.8244 (mt) REVERT: h 144 TYR cc_start: 0.9734 (m-80) cc_final: 0.9450 (m-80) REVERT: i 17 MET cc_start: 0.9170 (mpp) cc_final: 0.8878 (mpp) REVERT: i 144 TYR cc_start: 0.8260 (m-10) cc_final: 0.7848 (m-10) REVERT: j 25 PHE cc_start: 0.8876 (m-10) cc_final: 0.8476 (m-80) REVERT: j 53 MET cc_start: 0.7378 (mmp) cc_final: 0.6867 (mmm) REVERT: j 64 ILE cc_start: 0.8766 (tp) cc_final: 0.8545 (tp) REVERT: j 92 GLN cc_start: 0.7998 (mp10) cc_final: 0.7665 (mm110) REVERT: j 140 VAL cc_start: 0.9302 (p) cc_final: 0.8827 (m) REVERT: k 53 MET cc_start: 0.6656 (ttt) cc_final: 0.6404 (ttt) REVERT: k 61 MET cc_start: 0.7653 (ppp) cc_final: 0.7198 (ppp) REVERT: k 104 LEU cc_start: 0.9498 (tt) cc_final: 0.9276 (tp) REVERT: k 131 MET cc_start: 0.9063 (ttp) cc_final: 0.8818 (ppp) REVERT: l 28 MET cc_start: 0.7224 (mmp) cc_final: 0.6988 (mmp) REVERT: l 53 MET cc_start: 0.6099 (tmm) cc_final: 0.5458 (tpt) REVERT: m 61 MET cc_start: 0.8685 (mmt) cc_final: 0.8216 (tpp) REVERT: m 104 LEU cc_start: 0.9249 (mt) cc_final: 0.8886 (mt) REVERT: n 25 PHE cc_start: 0.9464 (m-80) cc_final: 0.9020 (m-10) REVERT: n 53 MET cc_start: 0.8336 (pmm) cc_final: 0.8022 (pmm) REVERT: n 54 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9241 (mtpt) REVERT: n 78 ASN cc_start: 0.7257 (m110) cc_final: 0.6851 (p0) REVERT: n 131 MET cc_start: 0.8272 (mmp) cc_final: 0.7599 (mmt) REVERT: o 47 MET cc_start: 0.8496 (ttp) cc_final: 0.7943 (tmm) REVERT: o 68 TYR cc_start: 0.8573 (m-10) cc_final: 0.8095 (m-80) REVERT: 1 34 MET cc_start: 0.9205 (mmp) cc_final: 0.8820 (mmm) REVERT: 1 108 ASP cc_start: 0.9482 (m-30) cc_final: 0.9222 (m-30) REVERT: 1 277 CYS cc_start: 0.8815 (t) cc_final: 0.8535 (t) REVERT: 1 318 MET cc_start: 0.9492 (mmp) cc_final: 0.9167 (mmm) REVERT: 1 340 MET cc_start: 0.8859 (tpp) cc_final: 0.8507 (tpp) REVERT: 1 346 MET cc_start: 0.8996 (ttm) cc_final: 0.8778 (tpp) REVERT: 1 461 LEU cc_start: 0.9476 (mt) cc_final: 0.9061 (pp) REVERT: 1 540 MET cc_start: 0.9224 (mtp) cc_final: 0.9007 (mtp) REVERT: 1 550 MET cc_start: 0.9658 (mtp) cc_final: 0.8994 (ttp) REVERT: 1 574 MET cc_start: 0.8986 (mtt) cc_final: 0.8710 (mmt) REVERT: 1 608 MET cc_start: 0.9300 (ptm) cc_final: 0.9009 (ppp) REVERT: 2 263 LEU cc_start: 0.9821 (tp) cc_final: 0.9579 (pp) REVERT: 2 306 MET cc_start: 0.9145 (tpt) cc_final: 0.8911 (tpp) REVERT: 2 318 MET cc_start: 0.9365 (mmp) cc_final: 0.8892 (mmm) REVERT: 2 340 MET cc_start: 0.9091 (ttm) cc_final: 0.8637 (ttm) REVERT: 2 346 MET cc_start: 0.9227 (tpt) cc_final: 0.8842 (tpp) REVERT: 2 465 TYR cc_start: 0.9342 (m-80) cc_final: 0.9067 (m-80) REVERT: 2 544 MET cc_start: 0.9661 (mtp) cc_final: 0.9228 (mmt) REVERT: 2 550 MET cc_start: 0.9666 (tpt) cc_final: 0.9136 (tpp) REVERT: 2 574 MET cc_start: 0.8427 (mpp) cc_final: 0.7934 (mpp) REVERT: 3 231 PHE cc_start: 0.9033 (t80) cc_final: 0.8548 (t80) REVERT: 3 238 MET cc_start: 0.9202 (ppp) cc_final: 0.8901 (ppp) REVERT: 3 248 PHE cc_start: 0.9519 (m-10) cc_final: 0.9218 (m-80) REVERT: 3 309 GLU cc_start: 0.9603 (tm-30) cc_final: 0.9326 (tm-30) REVERT: 3 356 MET cc_start: 0.7817 (tpt) cc_final: 0.7592 (tpt) REVERT: 3 367 ASP cc_start: 0.8937 (m-30) cc_final: 0.8632 (m-30) REVERT: 3 431 ASP cc_start: 0.9717 (t0) cc_final: 0.9278 (t0) REVERT: 3 435 MET cc_start: 0.9183 (mtm) cc_final: 0.8727 (ptp) REVERT: 3 449 LEU cc_start: 0.9749 (tp) cc_final: 0.9480 (pp) REVERT: 3 491 MET cc_start: 0.9517 (ptp) cc_final: 0.9269 (ptp) REVERT: 4 97 GLN cc_start: 0.9198 (pt0) cc_final: 0.8981 (pm20) REVERT: 4 180 MET cc_start: 0.9456 (tpp) cc_final: 0.9204 (tpp) REVERT: 4 187 GLN cc_start: 0.7732 (tt0) cc_final: 0.7366 (tm-30) REVERT: 4 234 MET cc_start: 0.8192 (tmm) cc_final: 0.7453 (tmm) REVERT: 4 279 LEU cc_start: 0.9896 (mm) cc_final: 0.9252 (mt) REVERT: 4 283 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8877 (mp0) REVERT: 4 299 ASP cc_start: 0.8703 (t0) cc_final: 0.8352 (t0) REVERT: 4 491 MET cc_start: 0.8558 (ptp) cc_final: 0.8267 (pmm) REVERT: 4 492 LEU cc_start: 0.9369 (mp) cc_final: 0.9070 (mp) REVERT: 5 214 LYS cc_start: 0.8671 (mttt) cc_final: 0.8261 (mtmt) REVERT: 5 270 GLU cc_start: 0.8861 (tp30) cc_final: 0.8538 (tp30) REVERT: 5 283 GLU cc_start: 0.9521 (mt-10) cc_final: 0.9241 (mt-10) REVERT: 5 356 MET cc_start: 0.9312 (ttt) cc_final: 0.9063 (tpp) REVERT: 5 453 GLU cc_start: 0.9428 (tt0) cc_final: 0.9173 (pt0) REVERT: 7 14 MET cc_start: 0.8952 (mmt) cc_final: 0.8719 (mmt) REVERT: 7 56 MET cc_start: 0.9092 (mmp) cc_final: 0.8693 (mmp) REVERT: 8 38 PHE cc_start: 0.9519 (t80) cc_final: 0.9042 (t80) REVERT: 8 132 MET cc_start: 0.7535 (mmp) cc_final: 0.6922 (mmm) REVERT: 8 207 MET cc_start: 0.9041 (mmm) cc_final: 0.8563 (mmm) REVERT: 9 72 MET cc_start: 0.9359 (tmm) cc_final: 0.8861 (tmm) REVERT: 9 76 MET cc_start: 0.9374 (mmp) cc_final: 0.9082 (mmp) REVERT: 9 124 LEU cc_start: 0.9653 (tp) cc_final: 0.9395 (pp) REVERT: T 102 MET cc_start: 0.9540 (mmm) cc_final: 0.9090 (mmm) REVERT: V 49 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8173 (mtt-85) REVERT: X 37 LEU cc_start: 0.9718 (tp) cc_final: 0.9458 (tp) REVERT: X 47 GLU cc_start: 0.9574 (mm-30) cc_final: 0.9318 (pt0) REVERT: X 57 ASN cc_start: 0.9273 (m110) cc_final: 0.8944 (m-40) REVERT: 6 23 HIS cc_start: 0.8683 (t-170) cc_final: 0.8321 (t-170) REVERT: 6 61 LEU cc_start: 0.7809 (tt) cc_final: 0.7451 (tp) REVERT: 6 134 ASN cc_start: 0.9381 (m-40) cc_final: 0.8976 (m110) REVERT: U 65 MET cc_start: 0.6045 (tpt) cc_final: 0.4066 (mtt) REVERT: U 239 LEU cc_start: 0.9237 (mt) cc_final: 0.8882 (tt) REVERT: U 289 PHE cc_start: 0.9177 (m-10) cc_final: 0.8833 (m-80) REVERT: d 44 ASP cc_start: 0.9546 (m-30) cc_final: 0.9246 (t0) REVERT: d 48 HIS cc_start: 0.8816 (m-70) cc_final: 0.8471 (m-70) REVERT: d 78 MET cc_start: 0.8942 (tpp) cc_final: 0.8702 (tpt) REVERT: d 138 MET cc_start: 0.9362 (mpp) cc_final: 0.9132 (mpp) REVERT: d 171 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8798 (tm-30) REVERT: d 176 MET cc_start: 0.8938 (mmp) cc_final: 0.8712 (mmm) REVERT: d 297 HIS cc_start: 0.9408 (t70) cc_final: 0.9076 (t70) REVERT: d 322 LYS cc_start: 0.9646 (tptm) cc_final: 0.9321 (tppt) REVERT: a 10 MET cc_start: 0.7949 (pmm) cc_final: 0.7494 (pmm) REVERT: a 362 MET cc_start: 0.8138 (ppp) cc_final: 0.7329 (ppp) REVERT: a 372 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8070 (p0) REVERT: a 382 GLN cc_start: 0.8542 (tp-100) cc_final: 0.7588 (tp-100) REVERT: a 408 PHE cc_start: 0.8901 (p90) cc_final: 0.8579 (p90) REVERT: a 430 MET cc_start: 0.8549 (mmp) cc_final: 0.8213 (mmm) REVERT: a 460 MET cc_start: 0.9055 (mmp) cc_final: 0.8726 (mmp) REVERT: a 545 MET cc_start: 0.9069 (mtp) cc_final: 0.8526 (mtp) REVERT: a 546 LYS cc_start: 0.8576 (mttt) cc_final: 0.8128 (mttt) REVERT: a 747 SER cc_start: 0.8596 (t) cc_final: 0.8079 (m) REVERT: a 809 TRP cc_start: 0.8692 (t60) cc_final: 0.8258 (t60) REVERT: c 439 MET cc_start: 0.9677 (mmp) cc_final: 0.9161 (mmm) REVERT: 0 34 MET cc_start: 0.7923 (mmp) cc_final: 0.7701 (mmm) REVERT: 0 108 ASP cc_start: 0.9368 (t70) cc_final: 0.9141 (t0) REVERT: 0 284 MET cc_start: 0.9119 (mmp) cc_final: 0.8668 (mmm) REVERT: 0 318 MET cc_start: 0.9430 (mmp) cc_final: 0.9163 (mmm) REVERT: 0 340 MET cc_start: 0.8747 (tpp) cc_final: 0.8004 (tpp) REVERT: 0 347 MET cc_start: 0.9179 (tpt) cc_final: 0.8920 (tpp) REVERT: 0 433 TRP cc_start: 0.8914 (t-100) cc_final: 0.8481 (t-100) REVERT: 0 540 MET cc_start: 0.8541 (pmm) cc_final: 0.8259 (pmm) REVERT: f 21 TRP cc_start: 0.8705 (t60) cc_final: 0.8405 (t60) REVERT: f 52 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9012 (mp0) REVERT: f 67 TYR cc_start: 0.8801 (m-80) cc_final: 0.8389 (t80) REVERT: f 70 PHE cc_start: 0.9157 (m-80) cc_final: 0.8697 (m-10) REVERT: s 153 MET cc_start: 0.5836 (tmm) cc_final: 0.5359 (tmm) REVERT: s 180 GLU cc_start: 0.9548 (tp30) cc_final: 0.9190 (tm-30) REVERT: s 181 MET cc_start: 0.6417 (tpp) cc_final: 0.6062 (tpp) REVERT: s 183 MET cc_start: 0.5734 (ptt) cc_final: 0.5174 (ptt) outliers start: 1 outliers final: 0 residues processed: 872 average time/residue: 0.5977 time to fit residues: 908.1005 Evaluate side-chains 694 residues out of total 7228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 693 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 9.9990 chunk 718 optimal weight: 6.9990 chunk 206 optimal weight: 0.0060 chunk 621 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 675 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 693 optimal weight: 7.9990 chunk 85 optimal weight: 0.0970 chunk 124 optimal weight: 5.9990 overall best weight: 2.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 90 ASN ** k 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 350 GLN ** 7 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN V 46 GLN 6 194 HIS ** U 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 ASN a 622 ASN a 767 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.054241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039556 restraints weight = 560719.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040309 restraints weight = 344473.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040907 restraints weight = 237761.817| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 68434 Z= 0.207 Angle : 0.652 13.609 92493 Z= 0.339 Chirality : 0.043 0.304 10483 Planarity : 0.004 0.060 11849 Dihedral : 4.455 39.086 9314 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 0.03 % Allowed : 0.43 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.84 % 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: 0.42 (0.09), residues: 8508 helix: 1.30 (0.07), residues: 4793 sheet: -0.31 (0.20), residues: 736 loop : -1.24 (0.12), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP b 67 HIS 0.006 0.001 HIS R 111 PHE 0.029 0.002 PHE f 33 TYR 0.038 0.001 TYR g 144 ARG 0.009 0.000 ARG n 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15613.99 seconds wall clock time: 274 minutes 35.80 seconds (16475.80 seconds total)