Starting phenix.real_space_refine on Sat Sep 28 17:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/09_2024/6ppf_20435.cif" } resolution = 3.4 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= 0.017 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: 5 Type Number sf(0) Gaussians P 2583 5.49 5 S 49 5.16 5 C 34973 2.51 5 N 13376 2.21 5 O 20854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.70s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71835 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 53094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2471, 53094 Classifications: {'RNA': 2471} Modifications used: {'rna2p_pur': 236, 'rna2p_pyr': 129, 'rna3p_pur': 1213, 'rna3p_pyr': 893} Link IDs: {'rna2p': 365, 'rna3p': 2105} Chain breaks: 12 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 45} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1684 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "D" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1265 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 2 Chain: "E" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1484 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 952 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 1 Chain: "P" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 846 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "U" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 739 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 555 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 29.35, per 1000 atoms: 0.41 Number of scatterers: 71835 At special positions: 0 Unit cell: (203.87, 196.359, 219.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 2583 15.00 O 20854 8.00 N 13376 7.00 C 34973 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 - 3.00 Amino acid : True - 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: 12.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 36 sheets defined 27.1% alpha, 15.7% beta 681 base pairs and 1275 stacking pairs defined. Time for finding SS restraints: 28.01 Creating SS restraints... Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.764A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 201' Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.646A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.528A pdb=" N LEU E 38 " --> pdb=" O PHE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.847A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 147 removed outlier: 3.517A pdb=" N LYS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.535A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 206 removed outlier: 4.144A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 31 Processing helix chain 'J' and resid 32 through 38 removed outlier: 3.708A pdb=" N ILE J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 72 Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.065A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.798A pdb=" N LEU K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 108 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 removed outlier: 3.708A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.807A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY L 26 " --> pdb=" O ILE L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 22 through 26' Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.668A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.594A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 41 removed outlier: 3.616A pdb=" N GLU N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 4.300A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 3.799A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 86 Processing helix chain 'N' and resid 87 through 90 Processing helix chain 'O' and resid 7 through 22 removed outlier: 3.592A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 78 removed outlier: 3.564A pdb=" N VAL O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 86 removed outlier: 3.696A pdb=" N LYS O 83 " --> pdb=" O GLU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 115 Processing helix chain 'P' and resid 6 through 12 Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.719A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU P 105 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 4.153A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG Q 13 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.867A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 69 removed outlier: 4.164A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET Q 40 " --> pdb=" O ASN Q 36 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS Q 41 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA Q 67 " --> pdb=" O THR Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 73 removed outlier: 3.546A pdb=" N GLY Q 73 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 70 through 73' Processing helix chain 'Q' and resid 76 through 81 Processing helix chain 'Q' and resid 92 through 97 Processing helix chain 'Q' and resid 103 through 118 removed outlier: 4.154A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA Q 110 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 Processing helix chain 'S' and resid 29 through 38 removed outlier: 4.169A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 62 removed outlier: 3.665A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA S 56 " --> pdb=" O LYS S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 4 through 7 No H-bonds generated for 'chain 'T' and resid 4 through 7' Processing helix chain 'T' and resid 14 through 21 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.991A pdb=" N VAL T 39 " --> pdb=" O ASN T 35 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER T 45 " --> pdb=" O ASP T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 17 removed outlier: 4.194A pdb=" N ASP U 16 " --> pdb=" O SER U 13 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS U 17 " --> pdb=" O GLY U 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 13 through 17' Processing helix chain 'Z' and resid 16 through 26 removed outlier: 3.574A pdb=" N ARG Z 20 " --> pdb=" O PRO Z 16 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.608A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 15 Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.617A pdb=" N ILE Y 6 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 15 removed outlier: 3.575A pdb=" N GLU Y 15 " --> pdb=" O THR Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 32 removed outlier: 3.589A pdb=" N GLU Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 54 removed outlier: 3.854A pdb=" N LYS Y 48 " --> pdb=" O ARG Y 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA Y 49 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 64 removed outlier: 3.684A pdb=" N ILE Y 62 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.811A pdb=" N ARG d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU d 29 " --> pdb=" O LYS d 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.938A pdb=" N THR C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.577A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 167 removed outlier: 4.499A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.576A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.809A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 27 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 28 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 186 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 15 through 16 removed outlier: 4.099A pdb=" N VAL D 15 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE D 23 " --> pdb=" O VAL D 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.681A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.140A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 125 removed outlier: 7.435A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'K' and resid 8 through 10 removed outlier: 7.020A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS K 59 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.944A pdb=" N ILE K 77 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.463A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE L 111 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.476A pdb=" N VAL L 123 " --> pdb=" O GLU L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 33 removed outlier: 3.563A pdb=" N THR N 32 " --> pdb=" O ALA N 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.998A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 55 through 57 Processing sheet with id=AC3, first strand: chain 'P' and resid 71 through 73 Processing sheet with id=AC4, first strand: chain 'P' and resid 71 through 73 removed outlier: 3.821A pdb=" N THR P 63 " --> pdb=" O LYS P 52 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS P 52 " --> pdb=" O THR P 63 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG P 65 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL P 50 " --> pdb=" O ARG P 65 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ILE P 67 " --> pdb=" O GLY P 48 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY P 48 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.141A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 73 through 75 Processing sheet with id=AC7, first strand: chain 'S' and resid 5 through 6 removed outlier: 6.893A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AD1, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.724A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.984A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AD5, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AD6, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.921A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG V 47 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 73 through 79 removed outlier: 3.545A pdb=" N SER V 88 " --> pdb=" O LYS V 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 34 through 37 removed outlier: 3.504A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'b' and resid 27 through 29 392 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1637 hydrogen bonds 2692 hydrogen bond angles 0 basepair planarities 681 basepair parallelities 1275 stacking parallelities Total time for adding SS restraints: 102.16 Time building geometry restraints manager: 15.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7677 1.32 - 1.44: 35394 1.44 - 1.56: 30356 1.56 - 1.69: 5152 1.69 - 1.81: 91 Bond restraints: 78670 Sorted by residual: bond pdb=" C ARG E 79 " pdb=" N SER E 80 " ideal model delta sigma weight residual 1.329 1.268 0.060 1.86e-02 2.89e+03 1.06e+01 bond pdb=" C HIS J 41 " pdb=" N LYS J 42 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.07e-02 2.33e+03 5.77e+00 bond pdb=" C3' U A1107 " pdb=" O3' U A1107 " ideal model delta sigma weight residual 1.427 1.457 -0.030 1.50e-02 4.44e+03 3.98e+00 bond pdb=" C5 A A1291 " pdb=" C6 A A1291 " ideal model delta sigma weight residual 1.406 1.368 0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C THR J 4 " pdb=" N PRO J 5 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.49e+00 ... (remaining 78665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.76: 118861 5.76 - 11.53: 167 11.53 - 17.29: 16 17.29 - 23.06: 6 23.06 - 28.82: 4 Bond angle restraints: 119054 Sorted by residual: angle pdb=" C LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta sigma weight residual 110.90 139.72 -28.82 1.58e+00 4.01e-01 3.33e+02 angle pdb=" C ILE O 90 " pdb=" CA ILE O 90 " pdb=" CB ILE O 90 " ideal model delta sigma weight residual 111.29 87.14 24.15 1.64e+00 3.72e-01 2.17e+02 angle pdb=" N ARG E 84 " pdb=" CA ARG E 84 " pdb=" C ARG E 84 " ideal model delta sigma weight residual 111.69 128.33 -16.64 1.23e+00 6.61e-01 1.83e+02 angle pdb=" C ILE R 22 " pdb=" CA ILE R 22 " pdb=" CB ILE R 22 " ideal model delta sigma weight residual 110.91 92.04 18.87 1.46e+00 4.69e-01 1.67e+02 angle pdb=" C PHE L 85 " pdb=" CA PHE L 85 " pdb=" CB PHE L 85 " ideal model delta sigma weight residual 109.33 85.95 23.38 1.97e+00 2.58e-01 1.41e+02 ... (remaining 119049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 43062 35.98 - 71.95: 6498 71.95 - 107.93: 777 107.93 - 143.91: 33 143.91 - 179.88: 49 Dihedral angle restraints: 50419 sinusoidal: 44468 harmonic: 5951 Sorted by residual: dihedral pdb=" C LEU Q 103 " pdb=" N LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta harmonic sigma weight residual -122.60 -163.99 41.39 0 2.50e+00 1.60e-01 2.74e+02 dihedral pdb=" N LEU Q 103 " pdb=" C LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta harmonic sigma weight residual 122.80 156.45 -33.65 0 2.50e+00 1.60e-01 1.81e+02 dihedral pdb=" C LYS D 56 " pdb=" N LYS D 56 " pdb=" CA LYS D 56 " pdb=" CB LYS D 56 " ideal model delta harmonic sigma weight residual -122.60 -92.06 -30.54 0 2.50e+00 1.60e-01 1.49e+02 ... (remaining 50416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 15406 0.334 - 0.667: 23 0.667 - 1.001: 2 1.001 - 1.334: 1 1.334 - 1.668: 1 Chirality restraints: 15433 Sorted by residual: chirality pdb=" CA LEU Q 103 " pdb=" N LEU Q 103 " pdb=" C LEU Q 103 " pdb=" CB LEU Q 103 " both_signs ideal model delta sigma weight residual False 2.51 0.84 1.67 2.00e-01 2.50e+01 6.95e+01 chirality pdb=" CA ALA J 60 " pdb=" N ALA J 60 " pdb=" C ALA J 60 " pdb=" CB ALA J 60 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CA ILE R 22 " pdb=" N ILE R 22 " pdb=" C ILE R 22 " pdb=" CB ILE R 22 " both_signs ideal model delta sigma weight residual False 2.43 3.16 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 15430 not shown) Planarity restraints: 5422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1712 " 0.038 2.00e-02 2.50e+03 1.76e-02 9.24e+00 pdb=" N9 G A1712 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G A1712 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A1712 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A1712 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A1712 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A1712 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A1712 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1712 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG P 24 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO P 25 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO P 25 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 25 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 179 " -0.030 2.00e-02 2.50e+03 1.53e-02 6.43e+00 pdb=" N9 A A 179 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A A 179 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A 179 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A A 179 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A A 179 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A A 179 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A A 179 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A 179 " 0.004 2.00e-02 2.50e+03 ... (remaining 5419 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 26 1.90 - 2.65: 3680 2.65 - 3.40: 86865 3.40 - 4.15: 227081 4.15 - 4.90: 316729 Nonbonded interactions: 634381 Sorted by model distance: nonbonded pdb=" O2 C A2094 " pdb=" N2 G A2474 " model vdw 1.152 2.496 nonbonded pdb=" O2' G A 903 " pdb=" CD2 PHE V 77 " model vdw 1.186 3.340 nonbonded pdb=" O6 G A2428 " pdb=" O6 G A2429 " model vdw 1.330 3.040 nonbonded pdb=" CB ILE Q 88 " pdb=" CD PRO R 51 " model vdw 1.398 3.870 nonbonded pdb=" N2 G A 967 " pdb=" N1 A A2298 " model vdw 1.443 3.200 ... (remaining 634376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 3.070 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: 2.210 Check model and map are aligned: 0.430 Set scattering table: 0.500 Process input model: 208.030 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.006 0.063 78670 Z= 0.385 Angle : 0.879 28.823 119054 Z= 0.475 Chirality : 0.052 1.668 15433 Planarity : 0.004 0.068 5422 Dihedral : 25.553 179.884 46589 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.04 % Favored : 90.08 % Rotamer: Outliers : 7.36 % Allowed : 11.04 % Favored : 81.60 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.14), residues: 2047 helix: -4.38 (0.12), residues: 495 sheet: -2.59 (0.25), residues: 347 loop : -2.92 (0.15), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 61 HIS 0.008 0.001 HIS C 142 PHE 0.020 0.002 PHE L 58 TYR 0.013 0.001 TYR C 83 ARG 0.007 0.000 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 595 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7501 (mmm160) REVERT: C 54 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7002 (tt0) REVERT: C 98 ASP cc_start: 0.8198 (p0) cc_final: 0.7979 (p0) REVERT: C 100 GLU cc_start: 0.8204 (pp20) cc_final: 0.7783 (pp20) REVERT: C 134 ASN cc_start: 0.8005 (m-40) cc_final: 0.6847 (t0) REVERT: C 171 TYR cc_start: 0.6291 (m-80) cc_final: 0.6004 (m-10) REVERT: D 56 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.5716 (pttt) REVERT: D 84 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6209 (mtp85) REVERT: D 86 VAL cc_start: 0.4709 (OUTLIER) cc_final: 0.4483 (m) REVERT: E 39 MET cc_start: 0.8159 (tmm) cc_final: 0.7901 (tmm) REVERT: E 97 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: J 15 LYS cc_start: 0.7706 (mttt) cc_final: 0.7347 (mmtp) REVERT: J 18 VAL cc_start: 0.8874 (t) cc_final: 0.8664 (t) REVERT: J 20 ASP cc_start: 0.8732 (p0) cc_final: 0.8434 (p0) REVERT: J 65 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6908 (pp) REVERT: J 75 TYR cc_start: 0.6646 (m-80) cc_final: 0.6017 (m-80) REVERT: J 92 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7605 (tm-30) REVERT: J 93 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7745 (mtm) REVERT: J 99 GLU cc_start: 0.7440 (mp0) cc_final: 0.6105 (mp0) REVERT: J 127 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7450 (ttm110) REVERT: J 137 LYS cc_start: 0.8507 (mttt) cc_final: 0.8247 (mmtp) REVERT: K 9 LYS cc_start: 0.7937 (ptmt) cc_final: 0.7628 (ptmm) REVERT: K 104 ARG cc_start: 0.6579 (tmm160) cc_final: 0.6208 (tpt90) REVERT: L 13 ARG cc_start: 0.8476 (mmt90) cc_final: 0.8191 (mmt180) REVERT: L 16 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7832 (ttp-170) REVERT: L 21 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7884 (mpt180) REVERT: L 55 MET cc_start: 0.5014 (ttt) cc_final: 0.4772 (ttt) REVERT: L 72 LYS cc_start: 0.8162 (mppt) cc_final: 0.7856 (mttm) REVERT: L 95 LEU cc_start: 0.7298 (tt) cc_final: 0.6779 (mt) REVERT: N 23 ASP cc_start: 0.7115 (m-30) cc_final: 0.6835 (m-30) REVERT: N 46 LYS cc_start: 0.8350 (mttt) cc_final: 0.8023 (mtpt) REVERT: O 59 LEU cc_start: 0.6256 (tp) cc_final: 0.5959 (tt) REVERT: O 84 ARG cc_start: 0.6703 (mtt-85) cc_final: 0.6483 (mtp85) REVERT: P 8 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6510 (mt) REVERT: P 44 GLN cc_start: 0.7225 (pt0) cc_final: 0.6956 (mm-40) REVERT: P 101 TYR cc_start: 0.8119 (m-10) cc_final: 0.7604 (m-80) REVERT: Q 11 ARG cc_start: 0.7587 (mmm160) cc_final: 0.7003 (tpp80) REVERT: Q 16 LYS cc_start: 0.8482 (mttt) cc_final: 0.8202 (mtpt) REVERT: Q 40 MET cc_start: 0.8569 (mtt) cc_final: 0.8349 (mtm) REVERT: Q 48 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7145 (ttp-170) REVERT: R 21 TYR cc_start: 0.4312 (OUTLIER) cc_final: 0.3649 (p90) REVERT: R 64 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7869 (ttpp) REVERT: R 71 ILE cc_start: 0.7926 (mt) cc_final: 0.7620 (pt) REVERT: R 81 ASN cc_start: 0.8471 (m-40) cc_final: 0.8140 (m-40) REVERT: R 98 GLU cc_start: 0.7335 (pm20) cc_final: 0.6759 (mp0) REVERT: S 4 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8382 (ttpp) REVERT: S 28 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7005 (tp40) REVERT: S 48 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7291 (tm-30) REVERT: S 57 ASN cc_start: 0.8040 (m-40) cc_final: 0.7699 (m110) REVERT: S 59 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7503 (mm-30) REVERT: S 90 MET cc_start: 0.5653 (mtt) cc_final: 0.5408 (mtt) REVERT: S 110 LYS cc_start: 0.7832 (tttt) cc_final: 0.7276 (tppt) REVERT: T 10 ARG cc_start: 0.8225 (ptp-170) cc_final: 0.7957 (ptp-110) REVERT: T 35 ASN cc_start: 0.8567 (m110) cc_final: 0.8354 (m-40) REVERT: T 40 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7929 (mtpt) REVERT: T 64 LYS cc_start: 0.6725 (mmtt) cc_final: 0.6326 (ptmt) REVERT: T 78 LYS cc_start: 0.7630 (pttt) cc_final: 0.7301 (ptmm) REVERT: U 4 LYS cc_start: 0.7273 (tttt) cc_final: 0.7028 (ttpt) REVERT: U 27 PHE cc_start: 0.7744 (m-80) cc_final: 0.7138 (m-10) REVERT: U 49 GLN cc_start: 0.4376 (OUTLIER) cc_final: 0.2897 (pp30) REVERT: U 59 GLN cc_start: 0.7572 (mt0) cc_final: 0.7321 (mm-40) REVERT: U 71 LEU cc_start: 0.8843 (mt) cc_final: 0.8589 (tp) REVERT: U 90 LYS cc_start: 0.7408 (ttpp) cc_final: 0.6822 (mtpt) REVERT: V 79 ARG cc_start: 0.5958 (OUTLIER) cc_final: 0.5402 (ptt180) REVERT: V 85 LYS cc_start: 0.7831 (mttt) cc_final: 0.7452 (mttt) REVERT: Z 3 LYS cc_start: 0.7637 (mmtp) cc_final: 0.7294 (tptt) REVERT: Z 9 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8298 (mmmm) REVERT: Z 10 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7503 (mmm-85) REVERT: Z 40 ASN cc_start: 0.7207 (t0) cc_final: 0.5989 (m110) REVERT: b 12 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7156 (mttt) REVERT: b 44 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7995 (mtpt) REVERT: b 52 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5958 (ptpp) REVERT: Y 23 GLU cc_start: 0.8438 (pp20) cc_final: 0.8060 (pp20) REVERT: Y 29 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7615 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7184 (tpt90) REVERT: Y 44 ARG cc_start: 0.7182 (mtp-110) cc_final: 0.6906 (ttp-110) REVERT: Y 48 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7926 (mtpt) REVERT: Y 53 MET cc_start: 0.8354 (mtm) cc_final: 0.8040 (mtp) REVERT: Y 59 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8139 (tp30) REVERT: Y 61 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7356 (mt-10) REVERT: d 1 MET cc_start: 0.6962 (mpp) cc_final: 0.6338 (mmp) REVERT: d 10 ARG cc_start: 0.8738 (ttt-90) cc_final: 0.8486 (ttt-90) REVERT: d 14 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8285 (mmtt) REVERT: d 36 ARG cc_start: 0.8030 (tmm-80) cc_final: 0.7825 (ttm170) outliers start: 128 outliers final: 15 residues processed: 672 average time/residue: 0.7929 time to fit residues: 863.8424 Evaluate side-chains 458 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 432 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 ARG Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 21 TYR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain b residue 52 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 267 optimal weight: 0.9990 chunk 415 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 GLN D 173 ASN E 46 GLN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 HIS J 54 HIS L 4 HIS L 35 HIS L 83 ASN L 126 ASN N 61 GLN O 15 HIS O 103 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS Q 37 GLN Q 66 ASN R 18 GLN R 81 ASN S 37 ASN T 35 ASN U 20 GLN U 64 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 78670 Z= 0.320 Angle : 0.793 14.050 119054 Z= 0.395 Chirality : 0.043 0.341 15433 Planarity : 0.006 0.072 5422 Dihedral : 25.632 179.251 42482 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.89 % Favored : 92.92 % Rotamer: Outliers : 5.00 % Allowed : 19.09 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.16), residues: 2047 helix: -3.30 (0.16), residues: 522 sheet: -2.27 (0.25), residues: 398 loop : -2.45 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 61 HIS 0.010 0.002 HIS C 53 PHE 0.027 0.002 PHE V 77 TYR 0.026 0.002 TYR R 2 ARG 0.008 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 437 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6629 (tt0) REVERT: C 100 GLU cc_start: 0.8153 (pp20) cc_final: 0.7862 (pp20) REVERT: C 180 GLU cc_start: 0.5880 (tm-30) cc_final: 0.5624 (tm-30) REVERT: C 183 MET cc_start: 0.8479 (mmm) cc_final: 0.7906 (mmm) REVERT: C 199 GLN cc_start: 0.8537 (mt0) cc_final: 0.8225 (mm110) REVERT: C 213 TRP cc_start: 0.5531 (m100) cc_final: 0.5246 (m100) REVERT: D 12 MET cc_start: 0.7805 (mmt) cc_final: 0.7346 (mmt) REVERT: D 13 THR cc_start: 0.7200 (p) cc_final: 0.6878 (p) REVERT: D 164 MET cc_start: 0.7661 (ptm) cc_final: 0.7387 (ptm) REVERT: E 39 MET cc_start: 0.8410 (tmm) cc_final: 0.8139 (tmm) REVERT: E 49 HIS cc_start: 0.8354 (p-80) cc_final: 0.8144 (p90) REVERT: E 82 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: E 194 ILE cc_start: 0.8335 (mm) cc_final: 0.7937 (mt) REVERT: J 13 GLU cc_start: 0.7552 (pm20) cc_final: 0.7087 (pm20) REVERT: J 15 LYS cc_start: 0.8221 (mttt) cc_final: 0.7895 (mmtp) REVERT: J 20 ASP cc_start: 0.8675 (p0) cc_final: 0.8472 (p0) REVERT: J 92 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7655 (tm-30) REVERT: J 93 MET cc_start: 0.8214 (mmm) cc_final: 0.7749 (tpp) REVERT: J 99 GLU cc_start: 0.7486 (mp0) cc_final: 0.6568 (mp0) REVERT: J 119 MET cc_start: 0.7458 (mtt) cc_final: 0.7057 (mtt) REVERT: J 127 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7608 (ttm110) REVERT: J 137 LYS cc_start: 0.8517 (mttt) cc_final: 0.8269 (mmtp) REVERT: K 9 LYS cc_start: 0.8049 (ptmt) cc_final: 0.7721 (ttmm) REVERT: L 3 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7490 (tt) REVERT: L 13 ARG cc_start: 0.8468 (mmt90) cc_final: 0.8190 (mmt180) REVERT: L 21 ARG cc_start: 0.8461 (mmt-90) cc_final: 0.8171 (mpt180) REVERT: L 72 LYS cc_start: 0.8187 (mppt) cc_final: 0.7782 (mttm) REVERT: L 126 ASN cc_start: 0.8489 (m110) cc_final: 0.8141 (m110) REVERT: N 46 LYS cc_start: 0.8231 (mttt) cc_final: 0.7949 (mtpt) REVERT: N 102 MET cc_start: 0.8274 (mpp) cc_final: 0.7916 (mpp) REVERT: N 110 ASP cc_start: 0.9066 (p0) cc_final: 0.8791 (p0) REVERT: P 9 GLU cc_start: 0.7493 (pt0) cc_final: 0.7061 (pt0) REVERT: P 74 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6721 (mm-30) REVERT: Q 16 LYS cc_start: 0.8488 (mttt) cc_final: 0.8263 (mmmt) REVERT: Q 48 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7339 (ttp-170) REVERT: Q 80 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7981 (mmt) REVERT: R 22 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7967 (pt) REVERT: R 64 LYS cc_start: 0.8390 (ttmt) cc_final: 0.8076 (ttpp) REVERT: R 71 ILE cc_start: 0.8043 (mt) cc_final: 0.7670 (pt) REVERT: R 81 ASN cc_start: 0.8672 (m-40) cc_final: 0.8411 (m-40) REVERT: S 4 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8479 (ttpp) REVERT: S 21 MET cc_start: 0.7382 (mmm) cc_final: 0.7161 (mmm) REVERT: S 48 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7650 (tm-30) REVERT: S 90 MET cc_start: 0.5577 (mtt) cc_final: 0.5306 (mtt) REVERT: S 110 LYS cc_start: 0.7995 (tttt) cc_final: 0.7449 (tppt) REVERT: T 35 ASN cc_start: 0.8412 (m-40) cc_final: 0.7892 (m110) REVERT: T 64 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6279 (ptmt) REVERT: T 77 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7454 (ttt180) REVERT: U 4 LYS cc_start: 0.7507 (tttt) cc_final: 0.7157 (tmmt) REVERT: U 27 PHE cc_start: 0.7935 (m-80) cc_final: 0.7299 (m-10) REVERT: U 39 ASN cc_start: 0.7426 (m-40) cc_final: 0.6682 (t0) REVERT: U 49 GLN cc_start: 0.4468 (OUTLIER) cc_final: 0.3055 (pm20) REVERT: U 59 GLN cc_start: 0.7818 (mt0) cc_final: 0.7428 (mm-40) REVERT: U 71 LEU cc_start: 0.8932 (mt) cc_final: 0.8650 (tp) REVERT: U 90 LYS cc_start: 0.7403 (ttpp) cc_final: 0.6620 (mtpt) REVERT: U 99 GLN cc_start: 0.6426 (mp10) cc_final: 0.6134 (mp10) REVERT: V 79 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5901 (ptt-90) REVERT: V 85 LYS cc_start: 0.7925 (mttt) cc_final: 0.7646 (mtpt) REVERT: Z 3 LYS cc_start: 0.7559 (mmtp) cc_final: 0.7282 (tptt) REVERT: Z 9 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8124 (mmmm) REVERT: Z 10 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7317 (mmm-85) REVERT: Z 40 ASN cc_start: 0.7079 (t0) cc_final: 0.5987 (m110) REVERT: b 12 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7204 (mttt) REVERT: b 16 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7680 (ttp-170) REVERT: b 44 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8088 (mtpt) REVERT: Y 16 GLN cc_start: 0.7499 (mp10) cc_final: 0.7114 (tm-30) REVERT: Y 19 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7781 (mmtm) REVERT: Y 23 GLU cc_start: 0.8361 (pp20) cc_final: 0.7950 (pp20) REVERT: Y 29 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7657 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7160 (tpt90) REVERT: Y 48 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7884 (mtpt) REVERT: d 1 MET cc_start: 0.6578 (mpp) cc_final: 0.6125 (mmp) REVERT: d 14 LYS cc_start: 0.8747 (ttmm) cc_final: 0.8385 (mmtm) REVERT: d 28 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7455 (mtm-85) outliers start: 87 outliers final: 51 residues processed: 496 average time/residue: 0.7717 time to fit residues: 635.0795 Evaluate side-chains 450 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 392 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 80 MET Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain Y residue 18 VAL Chi-restraints excluded: chain Y residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 450 optimal weight: 4.9990 chunk 371 optimal weight: 0.9980 chunk 413 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 334 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 134 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN N 12 GLN O 43 GLN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 78670 Z= 0.304 Angle : 0.724 11.143 119054 Z= 0.364 Chirality : 0.041 0.328 15433 Planarity : 0.006 0.082 5422 Dihedral : 25.494 177.899 42441 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 6.15 % Allowed : 20.47 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 2047 helix: -2.51 (0.19), residues: 502 sheet: -2.03 (0.24), residues: 412 loop : -2.21 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 213 HIS 0.009 0.002 HIS J 78 PHE 0.017 0.002 PHE D 119 TYR 0.021 0.002 TYR R 2 ARG 0.011 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 414 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7192 (mt-10) REVERT: C 87 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.5532 (mtm-85) REVERT: C 175 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5803 (ttm110) REVERT: C 199 GLN cc_start: 0.8520 (mt0) cc_final: 0.8298 (mm110) REVERT: D 12 MET cc_start: 0.7928 (mmt) cc_final: 0.7461 (mmt) REVERT: D 89 ASP cc_start: 0.6373 (p0) cc_final: 0.6159 (p0) REVERT: D 164 MET cc_start: 0.7801 (ptm) cc_final: 0.7338 (ptm) REVERT: E 39 MET cc_start: 0.8633 (tmm) cc_final: 0.8224 (tmm) REVERT: E 82 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: E 194 ILE cc_start: 0.8394 (mm) cc_final: 0.7998 (mt) REVERT: J 13 GLU cc_start: 0.7682 (pm20) cc_final: 0.7052 (pm20) REVERT: J 15 LYS cc_start: 0.8151 (mttt) cc_final: 0.7790 (mmtp) REVERT: J 20 ASP cc_start: 0.8655 (p0) cc_final: 0.8379 (p0) REVERT: J 50 ASP cc_start: 0.8287 (t0) cc_final: 0.7982 (t0) REVERT: J 99 GLU cc_start: 0.7618 (mp0) cc_final: 0.6504 (mp0) REVERT: J 119 MET cc_start: 0.7439 (mtt) cc_final: 0.7162 (mtt) REVERT: J 127 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7684 (ttp-110) REVERT: K 9 LYS cc_start: 0.8110 (ptmt) cc_final: 0.7820 (ttmm) REVERT: K 90 ASP cc_start: 0.5984 (t0) cc_final: 0.5736 (t0) REVERT: L 3 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7581 (tt) REVERT: L 13 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8220 (mmt90) REVERT: N 102 MET cc_start: 0.8290 (mpp) cc_final: 0.8044 (mpp) REVERT: N 110 ASP cc_start: 0.9106 (p0) cc_final: 0.8669 (p0) REVERT: P 74 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6677 (mm-30) REVERT: Q 12 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8124 (mtpp) REVERT: Q 56 ASP cc_start: 0.7355 (t0) cc_final: 0.7027 (m-30) REVERT: Q 78 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7779 (mtp85) REVERT: R 71 ILE cc_start: 0.7984 (mt) cc_final: 0.7502 (pt) REVERT: R 98 GLU cc_start: 0.7535 (pm20) cc_final: 0.6817 (mp0) REVERT: S 4 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8585 (ttpp) REVERT: S 21 MET cc_start: 0.7548 (mmm) cc_final: 0.7158 (mmm) REVERT: S 48 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7573 (tm-30) REVERT: S 90 MET cc_start: 0.5601 (mtt) cc_final: 0.5357 (mtt) REVERT: S 110 LYS cc_start: 0.7927 (tttt) cc_final: 0.7426 (tppt) REVERT: T 10 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.7705 (ptp-110) REVERT: T 29 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8261 (mm-30) REVERT: T 31 ASP cc_start: 0.7929 (t70) cc_final: 0.7599 (t0) REVERT: T 35 ASN cc_start: 0.8473 (m-40) cc_final: 0.8125 (m-40) REVERT: T 77 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7525 (ttt180) REVERT: U 4 LYS cc_start: 0.7719 (tttt) cc_final: 0.7332 (tmmt) REVERT: U 27 PHE cc_start: 0.7926 (m-80) cc_final: 0.7362 (m-10) REVERT: U 39 ASN cc_start: 0.7521 (m-40) cc_final: 0.7019 (t0) REVERT: U 59 GLN cc_start: 0.7900 (mt0) cc_final: 0.7509 (mm-40) REVERT: U 71 LEU cc_start: 0.8978 (mt) cc_final: 0.8748 (tp) REVERT: U 84 LYS cc_start: 0.6798 (ptmt) cc_final: 0.6227 (pttm) REVERT: U 90 LYS cc_start: 0.7398 (ttpp) cc_final: 0.6961 (mtpt) REVERT: V 79 ARG cc_start: 0.6957 (pmt170) cc_final: 0.6515 (ptt180) REVERT: V 85 LYS cc_start: 0.7847 (mttt) cc_final: 0.7595 (mtpt) REVERT: Z 3 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7483 (tptt) REVERT: Z 9 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8165 (mmmt) REVERT: Z 40 ASN cc_start: 0.6621 (t0) cc_final: 0.5931 (m110) REVERT: Z 44 ARG cc_start: 0.7730 (tpp80) cc_final: 0.7525 (tpp-160) REVERT: b 12 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7250 (mttt) REVERT: b 16 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7950 (ttp-170) REVERT: b 36 MET cc_start: 0.7060 (mmt) cc_final: 0.6484 (mmp) REVERT: b 44 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8147 (mtpt) REVERT: Y 16 GLN cc_start: 0.7738 (mp10) cc_final: 0.7355 (tm-30) REVERT: Y 19 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7718 (mmtm) REVERT: Y 23 GLU cc_start: 0.8389 (pp20) cc_final: 0.7988 (pp20) REVERT: Y 24 GLU cc_start: 0.7642 (tp30) cc_final: 0.7219 (tp30) REVERT: Y 29 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7672 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7358 (ttt180) cc_final: 0.7111 (tpt90) REVERT: Y 48 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7768 (mtpt) REVERT: d 1 MET cc_start: 0.6400 (mpp) cc_final: 0.5686 (mmp) outliers start: 107 outliers final: 71 residues processed: 491 average time/residue: 0.7467 time to fit residues: 615.2953 Evaluate side-chains 450 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 374 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 46 CYS Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 36 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 279 optimal weight: 0.8980 chunk 418 optimal weight: 4.9990 chunk 442 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 396 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS O 43 GLN ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS Q 116 GLN ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 78670 Z= 0.247 Angle : 0.670 11.038 119054 Z= 0.338 Chirality : 0.038 0.298 15433 Planarity : 0.005 0.076 5422 Dihedral : 25.387 179.583 42425 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.99 % Favored : 92.87 % Rotamer: Outliers : 5.92 % Allowed : 23.23 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 2047 helix: -2.16 (0.20), residues: 509 sheet: -1.76 (0.24), residues: 427 loop : -2.09 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 61 HIS 0.007 0.001 HIS C 53 PHE 0.013 0.002 PHE D 119 TYR 0.013 0.002 TYR N 3 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 388 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.7543 (tp40) cc_final: 0.7063 (tp40) REVERT: C 87 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5563 (mtm-85) REVERT: C 199 GLN cc_start: 0.8470 (mt0) cc_final: 0.8269 (mm-40) REVERT: D 12 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: D 89 ASP cc_start: 0.6579 (p0) cc_final: 0.6336 (p0) REVERT: D 164 MET cc_start: 0.7804 (ptm) cc_final: 0.7362 (ptm) REVERT: E 39 MET cc_start: 0.8632 (tmm) cc_final: 0.8184 (tmm) REVERT: E 82 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7915 (pt0) REVERT: E 194 ILE cc_start: 0.8346 (mm) cc_final: 0.7952 (mt) REVERT: J 12 ILE cc_start: 0.8493 (mp) cc_final: 0.8224 (mm) REVERT: J 13 GLU cc_start: 0.7470 (pm20) cc_final: 0.6826 (pm20) REVERT: J 15 LYS cc_start: 0.8139 (mttt) cc_final: 0.7789 (mmtp) REVERT: J 19 VAL cc_start: 0.8943 (t) cc_final: 0.8447 (m) REVERT: J 20 ASP cc_start: 0.8696 (p0) cc_final: 0.8451 (p0) REVERT: J 50 ASP cc_start: 0.8264 (t0) cc_final: 0.7932 (t0) REVERT: J 99 GLU cc_start: 0.7592 (mp0) cc_final: 0.6593 (mp0) REVERT: J 119 MET cc_start: 0.7398 (mtt) cc_final: 0.7081 (mtt) REVERT: J 127 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7663 (ttp-110) REVERT: J 142 GLU cc_start: 0.7425 (tp30) cc_final: 0.6652 (mp0) REVERT: K 9 LYS cc_start: 0.7961 (ptmt) cc_final: 0.7690 (ttmm) REVERT: L 3 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7608 (tt) REVERT: L 13 ARG cc_start: 0.8533 (mmt90) cc_final: 0.8237 (mmt90) REVERT: L 74 TYR cc_start: 0.7975 (m-80) cc_final: 0.7609 (m-10) REVERT: N 23 ASP cc_start: 0.8208 (t0) cc_final: 0.7603 (t0) REVERT: N 31 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: N 102 MET cc_start: 0.8268 (mpp) cc_final: 0.7998 (mpp) REVERT: N 110 ASP cc_start: 0.9080 (p0) cc_final: 0.8660 (p0) REVERT: P 60 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6642 (mm-30) REVERT: P 74 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6713 (mm-30) REVERT: P 101 TYR cc_start: 0.8185 (m-10) cc_final: 0.7902 (m-10) REVERT: Q 12 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8084 (mtpp) REVERT: Q 56 ASP cc_start: 0.7380 (t0) cc_final: 0.7077 (m-30) REVERT: Q 107 ASN cc_start: 0.8294 (m-40) cc_final: 0.8062 (m-40) REVERT: R 71 ILE cc_start: 0.8031 (mt) cc_final: 0.7582 (pt) REVERT: R 99 LYS cc_start: 0.7306 (tmtt) cc_final: 0.7064 (tptp) REVERT: S 4 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8553 (ttpp) REVERT: S 21 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7178 (mmm) REVERT: S 48 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7576 (tm-30) REVERT: S 110 LYS cc_start: 0.7907 (tttt) cc_final: 0.7401 (tppt) REVERT: T 10 ARG cc_start: 0.8295 (ptp-170) cc_final: 0.7691 (ptp-110) REVERT: T 35 ASN cc_start: 0.8346 (m-40) cc_final: 0.8052 (m-40) REVERT: T 77 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7657 (ttt180) REVERT: U 4 LYS cc_start: 0.7711 (tttt) cc_final: 0.7300 (pptt) REVERT: U 27 PHE cc_start: 0.7983 (m-80) cc_final: 0.7419 (m-10) REVERT: U 39 ASN cc_start: 0.7537 (m-40) cc_final: 0.7173 (t0) REVERT: U 59 GLN cc_start: 0.7947 (mt0) cc_final: 0.7383 (mm-40) REVERT: U 71 LEU cc_start: 0.9008 (mt) cc_final: 0.8643 (tp) REVERT: U 84 LYS cc_start: 0.6992 (ptmt) cc_final: 0.6330 (pttm) REVERT: U 90 LYS cc_start: 0.7252 (ttpp) cc_final: 0.6803 (mtpt) REVERT: U 99 GLN cc_start: 0.6308 (mp10) cc_final: 0.5941 (mp10) REVERT: V 79 ARG cc_start: 0.6912 (pmt170) cc_final: 0.6566 (ptt180) REVERT: V 85 LYS cc_start: 0.7963 (mttt) cc_final: 0.7647 (mtpt) REVERT: Z 3 LYS cc_start: 0.7708 (mmtp) cc_final: 0.7393 (tptt) REVERT: Z 9 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8129 (mmmt) REVERT: Z 44 ARG cc_start: 0.7671 (tpp80) cc_final: 0.7462 (tpp-160) REVERT: b 12 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7301 (mttt) REVERT: b 44 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8054 (mtpt) REVERT: Y 16 GLN cc_start: 0.7773 (mp10) cc_final: 0.7521 (tm-30) REVERT: Y 19 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7838 (mmtm) REVERT: Y 23 GLU cc_start: 0.8356 (pp20) cc_final: 0.7947 (pp20) REVERT: Y 24 GLU cc_start: 0.7643 (tp30) cc_final: 0.7282 (tp30) REVERT: Y 29 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7547 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7376 (ttt180) cc_final: 0.7132 (tpt90) REVERT: Y 48 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7576 (mtpt) REVERT: d 1 MET cc_start: 0.6191 (mpp) cc_final: 0.5520 (mmp) REVERT: d 40 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7549 (tptm) outliers start: 103 outliers final: 80 residues processed: 455 average time/residue: 0.7752 time to fit residues: 595.3876 Evaluate side-chains 461 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 374 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 46 CYS Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 329 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 397 optimal weight: 0.9980 chunk 111 optimal weight: 40.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN L 83 ASN O 43 GLN ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 78670 Z= 0.396 Angle : 0.797 11.765 119054 Z= 0.398 Chirality : 0.044 0.400 15433 Planarity : 0.006 0.071 5422 Dihedral : 25.473 179.199 42423 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.40 % Favored : 91.50 % Rotamer: Outliers : 7.19 % Allowed : 23.63 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.17), residues: 2047 helix: -2.20 (0.20), residues: 506 sheet: -1.89 (0.25), residues: 425 loop : -2.08 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 213 HIS 0.008 0.002 HIS C 53 PHE 0.021 0.002 PHE D 119 TYR 0.018 0.002 TYR C 83 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 381 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.5743 (mtm-85) REVERT: D 12 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7247 (mmt) REVERT: D 29 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.6647 (tp30) REVERT: D 164 MET cc_start: 0.7728 (ptm) cc_final: 0.7290 (ptm) REVERT: E 39 MET cc_start: 0.8619 (tmm) cc_final: 0.8226 (tmm) REVERT: E 82 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7956 (pt0) REVERT: E 194 ILE cc_start: 0.8383 (mm) cc_final: 0.8118 (mt) REVERT: J 12 ILE cc_start: 0.8539 (mp) cc_final: 0.8290 (mm) REVERT: J 13 GLU cc_start: 0.7469 (pm20) cc_final: 0.6821 (pm20) REVERT: J 15 LYS cc_start: 0.8125 (mttt) cc_final: 0.7726 (mmtp) REVERT: J 20 ASP cc_start: 0.8769 (p0) cc_final: 0.8477 (p0) REVERT: J 50 ASP cc_start: 0.8371 (t0) cc_final: 0.7944 (t0) REVERT: J 93 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: J 99 GLU cc_start: 0.7698 (mp0) cc_final: 0.7148 (mp0) REVERT: J 103 GLU cc_start: 0.6608 (pt0) cc_final: 0.6276 (pt0) REVERT: J 119 MET cc_start: 0.7331 (mtt) cc_final: 0.6952 (mtt) REVERT: J 127 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7756 (ttm110) REVERT: K 9 LYS cc_start: 0.7855 (ptmt) cc_final: 0.7596 (ttmm) REVERT: L 3 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7737 (tt) REVERT: L 13 ARG cc_start: 0.8524 (mmt90) cc_final: 0.8222 (mmt90) REVERT: L 74 TYR cc_start: 0.8086 (m-80) cc_final: 0.7732 (m-10) REVERT: N 23 ASP cc_start: 0.8121 (t0) cc_final: 0.7385 (t0) REVERT: N 27 ASN cc_start: 0.7547 (m-40) cc_final: 0.6942 (t0) REVERT: N 31 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: N 102 MET cc_start: 0.8426 (mpp) cc_final: 0.8014 (mpp) REVERT: N 110 ASP cc_start: 0.9113 (p0) cc_final: 0.8647 (p0) REVERT: Q 12 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8073 (mtpp) REVERT: Q 48 ARG cc_start: 0.7330 (ttp80) cc_final: 0.7091 (ttp-170) REVERT: Q 56 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: R 71 ILE cc_start: 0.8084 (mt) cc_final: 0.7573 (pt) REVERT: R 98 GLU cc_start: 0.7283 (pm20) cc_final: 0.6677 (mt-10) REVERT: S 4 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8600 (ttpp) REVERT: S 21 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7258 (mmm) REVERT: S 48 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7570 (tm-30) REVERT: S 110 LYS cc_start: 0.7977 (tttt) cc_final: 0.7510 (tppt) REVERT: T 10 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7493 (ptp-110) REVERT: T 31 ASP cc_start: 0.7899 (t70) cc_final: 0.7543 (t0) REVERT: T 35 ASN cc_start: 0.8506 (m-40) cc_final: 0.8178 (m-40) REVERT: T 77 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7676 (ttt180) REVERT: U 4 LYS cc_start: 0.7750 (tttt) cc_final: 0.7392 (pptt) REVERT: U 27 PHE cc_start: 0.8064 (m-80) cc_final: 0.7585 (m-10) REVERT: U 39 ASN cc_start: 0.7723 (m-40) cc_final: 0.7451 (t0) REVERT: U 59 GLN cc_start: 0.8015 (mt0) cc_final: 0.7638 (mm-40) REVERT: U 71 LEU cc_start: 0.8965 (mt) cc_final: 0.8496 (tp) REVERT: U 84 LYS cc_start: 0.7003 (ptmt) cc_final: 0.6462 (pttm) REVERT: U 90 LYS cc_start: 0.7339 (ttpp) cc_final: 0.6901 (mtpt) REVERT: U 99 GLN cc_start: 0.6312 (mp10) cc_final: 0.5934 (mp10) REVERT: V 79 ARG cc_start: 0.7121 (pmt170) cc_final: 0.6820 (ptt180) REVERT: V 80 PHE cc_start: 0.6810 (m-10) cc_final: 0.6584 (m-10) REVERT: V 85 LYS cc_start: 0.7936 (mttt) cc_final: 0.7590 (mtpt) REVERT: Z 3 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7225 (mmmt) REVERT: Z 9 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8360 (mmmt) REVERT: Z 38 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7160 (mp0) REVERT: Z 40 ASN cc_start: 0.6548 (t0) cc_final: 0.6042 (m-40) REVERT: b 12 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7246 (mttt) REVERT: b 44 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7998 (mtpt) REVERT: Y 19 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7827 (mptt) REVERT: Y 24 GLU cc_start: 0.7679 (tp30) cc_final: 0.7390 (tp30) REVERT: Y 29 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7523 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7509 (ttt180) cc_final: 0.7265 (tpt90) REVERT: Y 44 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7418 (ttp-110) REVERT: d 1 MET cc_start: 0.6348 (mpp) cc_final: 0.5658 (mmp) outliers start: 125 outliers final: 99 residues processed: 468 average time/residue: 0.7442 time to fit residues: 584.5029 Evaluate side-chains 479 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 370 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 28 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 46 CYS Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 259 optimal weight: 4.9990 chunk 109 optimal weight: 40.0000 chunk 443 optimal weight: 0.8980 chunk 367 optimal weight: 10.0000 chunk 205 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 232 optimal weight: 30.0000 overall best weight: 6.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN O 43 GLN ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 32 ASN ** b 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 78670 Z= 0.484 Angle : 0.880 14.434 119054 Z= 0.437 Chirality : 0.048 0.453 15433 Planarity : 0.007 0.075 5422 Dihedral : 25.578 179.948 42423 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.41 % Favored : 89.45 % Rotamer: Outliers : 8.28 % Allowed : 24.27 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 2047 helix: -2.31 (0.20), residues: 502 sheet: -1.99 (0.25), residues: 417 loop : -2.21 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 213 HIS 0.009 0.002 HIS C 58 PHE 0.024 0.002 PHE D 119 TYR 0.020 0.003 TYR N 3 ARG 0.010 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 363 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.7303 (mmtt) cc_final: 0.7058 (mmmt) REVERT: C 87 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.5841 (mtm-85) REVERT: C 100 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7598 (pp20) REVERT: C 183 MET cc_start: 0.8432 (mmm) cc_final: 0.7256 (mmm) REVERT: D 12 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7284 (mmt) REVERT: D 29 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: D 164 MET cc_start: 0.7686 (ptm) cc_final: 0.7279 (ptm) REVERT: E 39 MET cc_start: 0.8612 (tmm) cc_final: 0.8316 (tmm) REVERT: E 82 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: J 13 GLU cc_start: 0.7570 (pm20) cc_final: 0.7048 (pm20) REVERT: J 15 LYS cc_start: 0.8256 (mttt) cc_final: 0.7775 (mmtp) REVERT: J 20 ASP cc_start: 0.8820 (p0) cc_final: 0.8589 (p0) REVERT: J 50 ASP cc_start: 0.8377 (t0) cc_final: 0.7918 (t0) REVERT: J 99 GLU cc_start: 0.7840 (mp0) cc_final: 0.7283 (mp0) REVERT: J 119 MET cc_start: 0.7458 (mtt) cc_final: 0.7109 (mtt) REVERT: J 127 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7849 (ttm110) REVERT: K 9 LYS cc_start: 0.7744 (ptmt) cc_final: 0.7474 (ttmm) REVERT: L 3 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7788 (tt) REVERT: L 13 ARG cc_start: 0.8471 (mmt90) cc_final: 0.8163 (mmt90) REVERT: L 74 TYR cc_start: 0.8121 (m-80) cc_final: 0.7794 (m-10) REVERT: N 23 ASP cc_start: 0.8102 (t0) cc_final: 0.7363 (t0) REVERT: N 27 ASN cc_start: 0.7682 (m-40) cc_final: 0.7080 (t0) REVERT: N 31 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: N 46 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7429 (mttp) REVERT: N 102 MET cc_start: 0.8467 (mpp) cc_final: 0.8022 (mpp) REVERT: N 110 ASP cc_start: 0.9099 (p0) cc_final: 0.8713 (p0) REVERT: P 101 TYR cc_start: 0.8250 (m-10) cc_final: 0.8002 (m-10) REVERT: Q 12 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8048 (mtpp) REVERT: Q 19 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6776 (tmtt) REVERT: Q 56 ASP cc_start: 0.7385 (t0) cc_final: 0.7101 (m-30) REVERT: Q 95 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (mt) REVERT: S 4 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8576 (ttpp) REVERT: S 21 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7210 (mmm) REVERT: S 110 LYS cc_start: 0.8015 (tttt) cc_final: 0.7531 (tppt) REVERT: T 10 ARG cc_start: 0.8339 (ptp-170) cc_final: 0.7698 (ptp-110) REVERT: T 31 ASP cc_start: 0.8079 (t70) cc_final: 0.7584 (t0) REVERT: T 77 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7594 (ttt180) REVERT: U 59 GLN cc_start: 0.8080 (mt0) cc_final: 0.7692 (mm-40) REVERT: U 71 LEU cc_start: 0.8877 (mt) cc_final: 0.8514 (tp) REVERT: U 90 LYS cc_start: 0.7311 (ttpp) cc_final: 0.6832 (mtpt) REVERT: U 99 GLN cc_start: 0.6310 (mp10) cc_final: 0.5852 (mp10) REVERT: V 46 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6232 (t80) REVERT: V 79 ARG cc_start: 0.7180 (pmt170) cc_final: 0.6813 (ptt180) REVERT: V 85 LYS cc_start: 0.7926 (mttt) cc_final: 0.7574 (mtpt) REVERT: Z 3 LYS cc_start: 0.7749 (mmtp) cc_final: 0.7205 (mmmt) REVERT: Z 9 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8379 (mmmt) REVERT: Z 38 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7111 (mp0) REVERT: Z 40 ASN cc_start: 0.6579 (t0) cc_final: 0.5770 (m-40) REVERT: b 12 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7237 (mttt) REVERT: b 44 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7953 (mtpt) REVERT: Y 19 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7548 (mptt) REVERT: Y 24 GLU cc_start: 0.7682 (tp30) cc_final: 0.7400 (tp30) REVERT: Y 29 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7487 (mtt-85) REVERT: Y 44 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7306 (ttp-110) REVERT: d 1 MET cc_start: 0.6275 (mpp) cc_final: 0.5610 (mmp) outliers start: 144 outliers final: 110 residues processed: 463 average time/residue: 0.7411 time to fit residues: 581.1069 Evaluate side-chains 472 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 350 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 23 PHE Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 46 CYS Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Y residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 252 optimal weight: 30.0000 chunk 323 optimal weight: 8.9990 chunk 250 optimal weight: 30.0000 chunk 373 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 441 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN E 169 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 32 ASN ** b 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 78670 Z= 0.485 Angle : 0.872 11.594 119054 Z= 0.433 Chirality : 0.048 0.454 15433 Planarity : 0.007 0.085 5422 Dihedral : 25.554 179.579 42423 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.31 % Favored : 89.45 % Rotamer: Outliers : 8.11 % Allowed : 25.53 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.17), residues: 2047 helix: -2.31 (0.20), residues: 502 sheet: -2.01 (0.25), residues: 407 loop : -2.30 (0.17), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 213 HIS 0.009 0.002 HIS C 58 PHE 0.022 0.002 PHE D 119 TYR 0.019 0.002 TYR N 3 ARG 0.009 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 359 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 LYS cc_start: 0.7300 (mmtt) cc_final: 0.7050 (mmmt) REVERT: C 87 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.5977 (mtm-85) REVERT: C 183 MET cc_start: 0.8381 (mmm) cc_final: 0.7209 (mmm) REVERT: D 12 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7235 (mmt) REVERT: D 29 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: D 54 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6326 (m-30) REVERT: D 164 MET cc_start: 0.7701 (ptm) cc_final: 0.7289 (ptm) REVERT: E 39 MET cc_start: 0.8610 (tmm) cc_final: 0.8306 (tmm) REVERT: E 82 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: J 13 GLU cc_start: 0.7794 (pm20) cc_final: 0.7423 (pm20) REVERT: J 15 LYS cc_start: 0.8173 (mttt) cc_final: 0.7719 (mmtp) REVERT: J 20 ASP cc_start: 0.8830 (p0) cc_final: 0.8569 (p0) REVERT: J 50 ASP cc_start: 0.8324 (t0) cc_final: 0.7992 (t0) REVERT: J 99 GLU cc_start: 0.7940 (mp0) cc_final: 0.7380 (mp0) REVERT: J 127 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.7874 (ttm110) REVERT: K 9 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7456 (ttmm) REVERT: K 53 LYS cc_start: 0.7283 (mttt) cc_final: 0.6829 (tppt) REVERT: K 54 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8468 (mtmt) REVERT: K 90 ASP cc_start: 0.5699 (t0) cc_final: 0.5478 (t0) REVERT: L 3 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7759 (tt) REVERT: L 13 ARG cc_start: 0.8505 (mmt90) cc_final: 0.8226 (mmt90) REVERT: L 74 TYR cc_start: 0.8126 (m-80) cc_final: 0.7820 (m-10) REVERT: L 118 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.4803 (mp0) REVERT: N 23 ASP cc_start: 0.8107 (t0) cc_final: 0.7260 (t0) REVERT: N 27 ASN cc_start: 0.7855 (m-40) cc_final: 0.7303 (t0) REVERT: N 31 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: N 102 MET cc_start: 0.8485 (mpp) cc_final: 0.8062 (mpp) REVERT: N 110 ASP cc_start: 0.9090 (p0) cc_final: 0.8703 (p0) REVERT: Q 12 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8038 (mtpp) REVERT: Q 19 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6712 (tmtt) REVERT: Q 56 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: Q 100 VAL cc_start: 0.6359 (OUTLIER) cc_final: 0.6137 (t) REVERT: S 4 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8619 (ttpp) REVERT: S 21 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7385 (mmm) REVERT: S 110 LYS cc_start: 0.7998 (tttt) cc_final: 0.7527 (tppt) REVERT: T 31 ASP cc_start: 0.8026 (t70) cc_final: 0.7544 (t0) REVERT: T 77 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7551 (ttt180) REVERT: U 59 GLN cc_start: 0.8181 (mt0) cc_final: 0.7755 (mm-40) REVERT: U 60 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: U 71 LEU cc_start: 0.8841 (mt) cc_final: 0.8506 (tp) REVERT: U 90 LYS cc_start: 0.7349 (ttpp) cc_final: 0.6947 (mtpt) REVERT: V 46 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6176 (t80) REVERT: V 79 ARG cc_start: 0.7305 (pmt170) cc_final: 0.6837 (ptt180) REVERT: V 85 LYS cc_start: 0.7974 (mttt) cc_final: 0.7636 (mtpt) REVERT: Z 3 LYS cc_start: 0.7795 (mmtp) cc_final: 0.7215 (mmmt) REVERT: Z 9 LYS cc_start: 0.8658 (mmtt) cc_final: 0.7973 (mmtm) REVERT: Z 38 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7056 (mp0) REVERT: Z 40 ASN cc_start: 0.6580 (t0) cc_final: 0.5765 (m-40) REVERT: b 12 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7242 (mttt) REVERT: b 44 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7917 (mtpt) REVERT: Y 24 GLU cc_start: 0.7708 (tp30) cc_final: 0.7309 (tp30) REVERT: Y 29 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7510 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7155 (tpt90) cc_final: 0.6744 (tpt90) REVERT: Y 44 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7357 (ttp-110) REVERT: d 1 MET cc_start: 0.6280 (mpp) cc_final: 0.5640 (mmp) outliers start: 141 outliers final: 110 residues processed: 455 average time/residue: 0.7567 time to fit residues: 586.3430 Evaluate side-chains 474 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 348 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 81 HIS Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 141 TYR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 118 GLU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 57 PHE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain T residue 77 ARG Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 46 TYR Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 46 CYS Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain d residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 GLN b 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 78670 Z= 0.238 Angle : 0.680 10.845 119054 Z= 0.342 Chirality : 0.038 0.291 15433 Planarity : 0.005 0.068 5422 Dihedral : 25.318 178.755 42423 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.48 % Rotamer: Outliers : 6.10 % Allowed : 28.06 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.17), residues: 2047 helix: -1.93 (0.21), residues: 518 sheet: -1.86 (0.25), residues: 410 loop : -2.13 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP J 16 HIS 0.008 0.001 HIS C 53 PHE 0.015 0.002 PHE Y 30 TYR 0.014 0.002 TYR K 76 ARG 0.007 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 368 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.5848 (mtm-85) REVERT: C 183 MET cc_start: 0.8453 (mmm) cc_final: 0.7271 (mmm) REVERT: D 12 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7183 (mmt) REVERT: D 29 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: D 164 MET cc_start: 0.7706 (ptm) cc_final: 0.7318 (ptm) REVERT: E 39 MET cc_start: 0.8640 (tmm) cc_final: 0.8213 (tmm) REVERT: E 82 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: E 194 ILE cc_start: 0.8312 (mm) cc_final: 0.7937 (mt) REVERT: J 13 GLU cc_start: 0.7729 (pm20) cc_final: 0.7307 (pm20) REVERT: J 15 LYS cc_start: 0.8159 (mttt) cc_final: 0.7704 (mmtp) REVERT: J 50 ASP cc_start: 0.8333 (t0) cc_final: 0.8056 (t0) REVERT: J 99 GLU cc_start: 0.7917 (mp0) cc_final: 0.7177 (mp0) REVERT: J 127 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.7989 (ttm110) REVERT: J 142 GLU cc_start: 0.7441 (tp30) cc_final: 0.7146 (tp30) REVERT: K 9 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7661 (ttmm) REVERT: K 53 LYS cc_start: 0.7244 (mttt) cc_final: 0.6775 (tppt) REVERT: K 54 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8478 (mtmt) REVERT: K 90 ASP cc_start: 0.6251 (t0) cc_final: 0.5972 (t0) REVERT: L 3 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7777 (tt) REVERT: L 13 ARG cc_start: 0.8455 (mmt90) cc_final: 0.8207 (mmm-85) REVERT: L 74 TYR cc_start: 0.8034 (m-80) cc_final: 0.7655 (m-10) REVERT: N 23 ASP cc_start: 0.8055 (t0) cc_final: 0.7270 (t0) REVERT: N 27 ASN cc_start: 0.7472 (m-40) cc_final: 0.6868 (t0) REVERT: N 31 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: N 46 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7417 (mttp) REVERT: N 102 MET cc_start: 0.8391 (mpp) cc_final: 0.8037 (mpp) REVERT: N 110 ASP cc_start: 0.9030 (p0) cc_final: 0.8670 (p0) REVERT: O 13 LYS cc_start: 0.5393 (OUTLIER) cc_final: 0.5083 (ttpp) REVERT: P 60 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6476 (mm-30) REVERT: Q 12 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7936 (mtpp) REVERT: Q 19 LYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6550 (tmtt) REVERT: Q 56 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: Q 78 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7807 (mtp85) REVERT: Q 100 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6277 (t) REVERT: R 71 ILE cc_start: 0.8099 (mt) cc_final: 0.7622 (pt) REVERT: S 4 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8422 (ttpp) REVERT: S 21 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7183 (mmm) REVERT: S 48 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7532 (tm-30) REVERT: S 110 LYS cc_start: 0.7981 (tttt) cc_final: 0.7522 (tppt) REVERT: T 10 ARG cc_start: 0.8374 (ptp-170) cc_final: 0.7748 (ptp-110) REVERT: T 31 ASP cc_start: 0.7931 (t70) cc_final: 0.7530 (t0) REVERT: U 59 GLN cc_start: 0.8206 (mt0) cc_final: 0.7703 (mm-40) REVERT: U 71 LEU cc_start: 0.8918 (mt) cc_final: 0.8558 (tp) REVERT: U 90 LYS cc_start: 0.7213 (ttpp) cc_final: 0.6815 (mtpt) REVERT: V 79 ARG cc_start: 0.7210 (pmt170) cc_final: 0.6820 (ptt180) REVERT: V 80 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5924 (m-10) REVERT: V 85 LYS cc_start: 0.7911 (mttt) cc_final: 0.7645 (mtpt) REVERT: Z 3 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7222 (mmmt) REVERT: Z 9 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8212 (mmmt) REVERT: Z 38 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7022 (mp0) REVERT: b 12 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7184 (mttt) REVERT: b 44 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7805 (mtpt) REVERT: b 52 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6909 (pttm) REVERT: Y 23 GLU cc_start: 0.8277 (pp20) cc_final: 0.7988 (pp20) REVERT: Y 24 GLU cc_start: 0.7606 (tp30) cc_final: 0.7340 (tp30) REVERT: Y 29 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7415 (mtt-85) REVERT: Y 44 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7276 (ttp-110) REVERT: d 1 MET cc_start: 0.5991 (mpp) cc_final: 0.5478 (mmp) outliers start: 106 outliers final: 79 residues processed: 441 average time/residue: 0.8212 time to fit residues: 620.8430 Evaluate side-chains 449 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 356 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 ARG Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 57 PHE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 411 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 371 optimal weight: 5.9990 chunk 389 optimal weight: 1.9990 chunk 409 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 32 ASN Y 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 78670 Z= 0.288 Angle : 0.707 11.294 119054 Z= 0.355 Chirality : 0.039 0.330 15433 Planarity : 0.005 0.068 5422 Dihedral : 25.310 178.988 42423 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.14 % Favored : 90.82 % Rotamer: Outliers : 6.56 % Allowed : 27.72 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.18), residues: 2047 helix: -1.84 (0.21), residues: 513 sheet: -1.85 (0.25), residues: 413 loop : -2.08 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 213 HIS 0.008 0.001 HIS C 53 PHE 0.014 0.002 PHE D 119 TYR 0.013 0.002 TYR C 83 ARG 0.007 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 359 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.5949 (mtm-85) REVERT: C 183 MET cc_start: 0.8423 (mmm) cc_final: 0.7234 (mmm) REVERT: D 12 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7173 (mmt) REVERT: D 29 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6552 (tp30) REVERT: D 54 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.5969 (m-30) REVERT: D 164 MET cc_start: 0.7637 (ptm) cc_final: 0.7248 (ptm) REVERT: E 39 MET cc_start: 0.8635 (tmm) cc_final: 0.8229 (tmm) REVERT: E 82 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: E 194 ILE cc_start: 0.8288 (mm) cc_final: 0.7903 (mt) REVERT: J 13 GLU cc_start: 0.7698 (pm20) cc_final: 0.7314 (pm20) REVERT: J 15 LYS cc_start: 0.8154 (mttt) cc_final: 0.7704 (mmtp) REVERT: J 50 ASP cc_start: 0.8358 (t0) cc_final: 0.8128 (t0) REVERT: J 99 GLU cc_start: 0.7928 (mp0) cc_final: 0.7346 (mp0) REVERT: J 127 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8046 (ttm110) REVERT: J 142 GLU cc_start: 0.7341 (tp30) cc_final: 0.7016 (tp30) REVERT: K 9 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7589 (ttmm) REVERT: K 53 LYS cc_start: 0.7280 (mttt) cc_final: 0.6778 (tppt) REVERT: K 54 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8460 (mtmt) REVERT: L 3 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7752 (tt) REVERT: L 13 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8199 (mmm-85) REVERT: L 74 TYR cc_start: 0.8077 (m-80) cc_final: 0.7615 (m-10) REVERT: N 23 ASP cc_start: 0.8006 (t0) cc_final: 0.7093 (t0) REVERT: N 27 ASN cc_start: 0.7565 (m-40) cc_final: 0.6941 (t0) REVERT: N 31 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: N 46 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7506 (mttp) REVERT: N 102 MET cc_start: 0.8374 (mpp) cc_final: 0.8015 (mpp) REVERT: N 110 ASP cc_start: 0.9127 (p0) cc_final: 0.8736 (p0) REVERT: O 13 LYS cc_start: 0.5441 (OUTLIER) cc_final: 0.5152 (ttpp) REVERT: Q 12 LYS cc_start: 0.8439 (mtpt) cc_final: 0.7957 (mtpp) REVERT: Q 19 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6564 (tmtt) REVERT: Q 56 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7115 (m-30) REVERT: Q 100 VAL cc_start: 0.6459 (OUTLIER) cc_final: 0.6235 (t) REVERT: R 71 ILE cc_start: 0.8084 (mt) cc_final: 0.7573 (pt) REVERT: S 4 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8501 (ttpp) REVERT: S 21 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7209 (mmm) REVERT: S 110 LYS cc_start: 0.7985 (tttt) cc_final: 0.7508 (tppt) REVERT: T 10 ARG cc_start: 0.8379 (ptp-170) cc_final: 0.7731 (ptp-110) REVERT: T 31 ASP cc_start: 0.7988 (t70) cc_final: 0.7612 (t0) REVERT: T 35 ASN cc_start: 0.8625 (m-40) cc_final: 0.8246 (m110) REVERT: U 59 GLN cc_start: 0.8131 (mt0) cc_final: 0.7691 (mm-40) REVERT: U 71 LEU cc_start: 0.8869 (mt) cc_final: 0.8509 (tp) REVERT: U 90 LYS cc_start: 0.7258 (ttpp) cc_final: 0.6839 (mtpt) REVERT: V 79 ARG cc_start: 0.7222 (pmt170) cc_final: 0.6822 (ptt180) REVERT: V 80 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6037 (m-10) REVERT: V 85 LYS cc_start: 0.8009 (mttt) cc_final: 0.7675 (mtpt) REVERT: Z 3 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7222 (mmmt) REVERT: Z 9 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8253 (mmmt) REVERT: Z 38 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7024 (mp0) REVERT: b 12 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7197 (mttt) REVERT: b 44 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7836 (mtpt) REVERT: b 52 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6908 (pttm) REVERT: Y 23 GLU cc_start: 0.8296 (pp20) cc_final: 0.7916 (pp20) REVERT: Y 24 GLU cc_start: 0.7633 (tp30) cc_final: 0.7303 (tp30) REVERT: Y 29 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7439 (mtt-85) REVERT: Y 44 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7321 (ttp-110) REVERT: d 1 MET cc_start: 0.6017 (mpp) cc_final: 0.5452 (mmp) outliers start: 114 outliers final: 91 residues processed: 435 average time/residue: 0.7396 time to fit residues: 544.1804 Evaluate side-chains 461 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 354 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 72 LYS Chi-restraints excluded: chain L residue 76 VAL Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 13 LYS Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 57 PHE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 4.9990 chunk 434 optimal weight: 9.9990 chunk 265 optimal weight: 0.0040 chunk 206 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 456 optimal weight: 1.9990 chunk 419 optimal weight: 5.9990 chunk 363 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 78670 Z= 0.172 Angle : 0.612 10.436 119054 Z= 0.308 Chirality : 0.035 0.264 15433 Planarity : 0.005 0.067 5422 Dihedral : 25.159 179.904 42423 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 5.23 % Allowed : 28.98 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.18), residues: 2047 helix: -1.55 (0.22), residues: 496 sheet: -1.64 (0.25), residues: 410 loop : -1.90 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 16 HIS 0.007 0.001 HIS C 142 PHE 0.012 0.001 PHE P 77 TYR 0.013 0.001 TYR K 76 ARG 0.007 0.000 ARG J 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 379 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.5854 (mtm-85) REVERT: C 183 MET cc_start: 0.8468 (mmm) cc_final: 0.7288 (mmm) REVERT: D 12 MET cc_start: 0.7718 (mmt) cc_final: 0.7087 (mmt) REVERT: D 164 MET cc_start: 0.7626 (ptm) cc_final: 0.7230 (ptm) REVERT: E 39 MET cc_start: 0.8622 (tmm) cc_final: 0.8196 (tmm) REVERT: E 82 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: E 150 LYS cc_start: 0.7258 (ttmm) cc_final: 0.6594 (mttt) REVERT: E 194 ILE cc_start: 0.8318 (mm) cc_final: 0.7958 (mt) REVERT: J 8 ASN cc_start: 0.7694 (p0) cc_final: 0.7494 (p0) REVERT: J 13 GLU cc_start: 0.7622 (pm20) cc_final: 0.7251 (pm20) REVERT: J 15 LYS cc_start: 0.8015 (mttt) cc_final: 0.7666 (mmtp) REVERT: J 50 ASP cc_start: 0.8329 (t0) cc_final: 0.8074 (t0) REVERT: J 99 GLU cc_start: 0.7908 (mp0) cc_final: 0.7119 (mp0) REVERT: J 127 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.7977 (ttm110) REVERT: K 53 LYS cc_start: 0.7248 (mttt) cc_final: 0.6782 (tppt) REVERT: K 54 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8447 (mtmt) REVERT: L 3 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7780 (tt) REVERT: L 13 ARG cc_start: 0.8375 (mmt90) cc_final: 0.8148 (mmm-85) REVERT: L 74 TYR cc_start: 0.7974 (m-80) cc_final: 0.7492 (m-10) REVERT: N 23 ASP cc_start: 0.7985 (t0) cc_final: 0.7132 (t0) REVERT: N 27 ASN cc_start: 0.7292 (m-40) cc_final: 0.6699 (t0) REVERT: N 31 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: N 46 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7360 (mttp) REVERT: N 72 ASN cc_start: 0.7312 (t0) cc_final: 0.6196 (m-40) REVERT: N 102 MET cc_start: 0.8355 (mpp) cc_final: 0.7942 (mpp) REVERT: N 110 ASP cc_start: 0.8988 (p0) cc_final: 0.8625 (p0) REVERT: O 38 LYS cc_start: 0.6191 (tptt) cc_final: 0.5847 (mmtp) REVERT: Q 12 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7899 (mtpp) REVERT: Q 19 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6446 (tmtt) REVERT: Q 56 ASP cc_start: 0.7320 (t0) cc_final: 0.7045 (m-30) REVERT: Q 116 GLN cc_start: 0.6923 (tt0) cc_final: 0.6691 (tt0) REVERT: S 4 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8433 (ttpp) REVERT: S 21 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7143 (mmm) REVERT: S 48 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7539 (tm-30) REVERT: S 110 LYS cc_start: 0.7928 (tttt) cc_final: 0.7491 (tppt) REVERT: T 10 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7875 (ptp-110) REVERT: T 29 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8021 (mm-30) REVERT: U 59 GLN cc_start: 0.8049 (mt0) cc_final: 0.7626 (mm-40) REVERT: U 71 LEU cc_start: 0.8893 (mt) cc_final: 0.8524 (tp) REVERT: U 90 LYS cc_start: 0.7181 (ttpp) cc_final: 0.6861 (mtpt) REVERT: V 79 ARG cc_start: 0.7191 (pmt170) cc_final: 0.6899 (ptt180) REVERT: V 80 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6080 (m-10) REVERT: V 85 LYS cc_start: 0.7926 (mttt) cc_final: 0.7574 (mtpt) REVERT: Z 3 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7154 (mmmt) REVERT: Z 9 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8198 (mmmt) REVERT: Z 38 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6998 (mp0) REVERT: b 12 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7117 (mttt) REVERT: b 44 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7930 (mttm) REVERT: b 52 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6915 (pttm) REVERT: Y 24 GLU cc_start: 0.7577 (tp30) cc_final: 0.7333 (tp30) REVERT: Y 29 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7560 (mtt-85) REVERT: Y 42 ARG cc_start: 0.7006 (tpt90) cc_final: 0.6682 (tpt90) REVERT: Y 44 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7184 (ttp-110) REVERT: Y 45 GLU cc_start: 0.8283 (tp30) cc_final: 0.8027 (tt0) REVERT: Y 52 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7921 (ttm110) REVERT: d 1 MET cc_start: 0.6052 (mpp) cc_final: 0.5379 (mmp) outliers start: 91 outliers final: 67 residues processed: 443 average time/residue: 0.7356 time to fit residues: 545.6150 Evaluate side-chains 441 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 365 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 97 TYR Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 54 LYS Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 68 ASN Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 19 LYS Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 57 PHE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 THR Chi-restraints excluded: chain S residue 83 LYS Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 43 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 80 PHE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 52 HIS Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 52 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 7.9990 chunk 387 optimal weight: 2.9990 chunk 111 optimal weight: 40.0000 chunk 335 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 373 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN E 169 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN Z 32 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112298 restraints weight = 133427.767| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.22 r_work: 0.3232 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 78670 Z= 0.374 Angle : 0.764 11.861 119054 Z= 0.381 Chirality : 0.042 0.382 15433 Planarity : 0.006 0.067 5422 Dihedral : 25.275 179.904 42423 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.62 % Favored : 90.33 % Rotamer: Outliers : 5.64 % Allowed : 29.33 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 2047 helix: -1.76 (0.21), residues: 504 sheet: -1.88 (0.25), residues: 420 loop : -2.04 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 213 HIS 0.009 0.002 HIS C 58 PHE 0.035 0.002 PHE Y 30 TYR 0.021 0.002 TYR C 62 ARG 0.008 0.001 ARG J 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12395.58 seconds wall clock time: 218 minutes 34.02 seconds (13114.02 seconds total)