Starting phenix.real_space_refine on Sun Sep 29 20:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sj6_10212/09_2024/6sj6_10212.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 2683 5.49 5 Mg 56 5.21 5 S 46 5.16 5 C 38599 2.51 5 N 14481 2.21 5 O 22428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 78296 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 55399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2585, 55399 Inner-chain residues flagged as termini: ['pdbres=" U A 233 "', 'pdbres=" U A 690 "', 'pdbres=" C A 764 "', 'pdbres=" G A 937 "', 'pdbres=" G A1156 "', 'pdbres=" C A1595 "', 'pdbres=" A A1923 "', 'pdbres=" A A1954 "', 'pdbres=" C A2210 "', 'pdbres=" C A2241 "', 'pdbres=" U A2825 "'] Classifications: {'RNA': 2585} Modifications used: {'5*END': 12, 'rna2p_pur': 283, 'rna2p_pyr': 137, 'rna3p_pur': 1201, 'rna3p_pyr': 964} Link IDs: {'rna2p': 420, 'rna3p': 2164} Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2380 Inner-chain residues flagged as termini: ['pdbres=" A B 44 "'] Classifications: {'RNA': 112} Modifications used: {'5*END': 2, 'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "D" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1863 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain breaks: 1 Chain: "E" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1637 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 8, 'TRANS': 207} Chain: "F" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1540 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 187} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1099 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "P" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1097 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "R" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 109} Chain: "S" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 837 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "V" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "W" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 725 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "X" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 738 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "Y" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 458 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 2 Chain: "Z" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "0" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "4" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain breaks: 1 Chain: "6" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 500 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "9" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 908 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Unusual residues: {' K': 3, ' MG': 56} Classifications: {'undetermined': 59} Link IDs: {None: 58} Time building chain proxies: 33.12, per 1000 atoms: 0.42 Number of scatterers: 78296 At special positions: 0 Unit cell: (211.068, 229.944, 207.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 46 16.00 P 2683 15.00 Mg 56 11.99 O 22428 8.00 N 14481 7.00 C 38599 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: 13.49 Conformation dependent library (CDL) restraints added in 3.0 seconds 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 36 sheets defined 20.1% alpha, 13.7% beta 373 base pairs and 1309 stacking pairs defined. Time for finding SS restraints: 27.47 Creating SS restraints... Processing helix chain 'D' and resid 206 through 214 removed outlier: 3.601A pdb=" N SER D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.676A pdb=" N HIS E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'F' and resid 29 through 34 removed outlier: 3.944A pdb=" N LEU F 33 " --> pdb=" O ASN F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 103 through 118 removed outlier: 4.824A pdb=" N ALA F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 111 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 140 through 145 removed outlier: 3.958A pdb=" N SER F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 Processing helix chain 'M' and resid 25 through 34 removed outlier: 4.236A pdb=" N GLU M 32 " --> pdb=" O ARG M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.575A pdb=" N ARG M 94 " --> pdb=" O GLY M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 105 removed outlier: 3.859A pdb=" N LEU M 101 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER M 105 " --> pdb=" O LEU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 121 Processing helix chain 'N' and resid 103 through 107 Processing helix chain 'N' and resid 111 through 116 removed outlier: 3.568A pdb=" N VAL N 115 " --> pdb=" O PHE N 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 83 removed outlier: 3.797A pdb=" N ASN O 83 " --> pdb=" O ASP O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 80 through 83' Processing helix chain 'O' and resid 92 through 99 removed outlier: 3.649A pdb=" N SER O 99 " --> pdb=" O LEU O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 137 Processing helix chain 'P' and resid 44 through 56 removed outlier: 3.590A pdb=" N SER P 49 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA P 53 " --> pdb=" O SER P 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET P 54 " --> pdb=" O ALA P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 123 removed outlier: 4.023A pdb=" N ALA P 114 " --> pdb=" O SER P 110 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA P 121 " --> pdb=" O ALA P 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HIS P 123 " --> pdb=" O ARG P 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 28 removed outlier: 4.375A pdb=" N ALA Q 15 " --> pdb=" O ASP Q 11 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP Q 19 " --> pdb=" O ALA Q 15 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Q 22 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 Processing helix chain 'Q' and resid 39 through 44 removed outlier: 3.818A pdb=" N VAL Q 44 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.532A pdb=" N ILE Q 48 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR Q 49 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS Q 53 " --> pdb=" O THR Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 62 Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'R' and resid 58 through 62 removed outlier: 3.881A pdb=" N ASP R 62 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 74 removed outlier: 3.869A pdb=" N ALA R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 84 removed outlier: 3.653A pdb=" N LYS R 82 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 84' Processing helix chain 'R' and resid 104 through 115 removed outlier: 3.906A pdb=" N ALA R 111 " --> pdb=" O ALA R 107 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 11 removed outlier: 3.825A pdb=" N VAL S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 14 Processing helix chain 'T' and resid 14 through 19 removed outlier: 3.973A pdb=" N ILE T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.506A pdb=" N HIS T 29 " --> pdb=" O GLY T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 50 removed outlier: 4.304A pdb=" N GLN T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET T 40 " --> pdb=" O LYS T 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS T 41 " --> pdb=" O GLN T 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY T 43 " --> pdb=" O VAL T 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG T 48 " --> pdb=" O GLN T 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 64 removed outlier: 4.311A pdb=" N ARG T 58 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS T 59 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU T 60 " --> pdb=" O ASP T 56 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 72 removed outlier: 3.530A pdb=" N GLN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 67 through 72' Processing helix chain 'T' and resid 76 through 87 removed outlier: 3.515A pdb=" N LEU T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS T 84 " --> pdb=" O MET T 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS T 85 " --> pdb=" O ASN T 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 86 " --> pdb=" O GLY T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 94 through 100 Processing helix chain 'T' and resid 103 through 116 removed outlier: 3.735A pdb=" N ALA T 113 " --> pdb=" O LEU T 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.525A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU V 19 " --> pdb=" O ARG V 15 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 38 Processing helix chain 'V' and resid 43 through 52 removed outlier: 4.374A pdb=" N LYS V 49 " --> pdb=" O PRO V 45 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL V 50 " --> pdb=" O VAL V 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 51 " --> pdb=" O ILE V 47 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET V 52 " --> pdb=" O GLU V 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 22 Processing helix chain 'W' and resid 35 through 46 removed outlier: 3.625A pdb=" N MET W 40 " --> pdb=" O THR W 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA W 41 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU W 44 " --> pdb=" O MET W 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 22 Processing helix chain 'Y' and resid 23 through 25 No H-bonds generated for 'chain 'Y' and resid 23 through 25' Processing helix chain 'Y' and resid 45 through 54 removed outlier: 3.587A pdb=" N LYS Y 50 " --> pdb=" O VAL Y 46 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL Y 51 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG Y 53 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 34 removed outlier: 3.743A pdb=" N ILE 1 18 " --> pdb=" O ILE 1 14 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS 1 19 " --> pdb=" O GLU 1 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER 1 20 " --> pdb=" O GLU 1 16 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU 1 28 " --> pdb=" O GLU 1 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE 1 30 " --> pdb=" O PHE 1 26 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU 1 32 " --> pdb=" O LEU 1 28 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 54 removed outlier: 4.344A pdb=" N THR 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG 1 47 " --> pdb=" O ILE 1 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE 1 50 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG 1 52 " --> pdb=" O LYS 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 58 through 64 removed outlier: 3.784A pdb=" N GLN 1 64 " --> pdb=" O ARG 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 27 Processing helix chain '2' and resid 42 through 48 removed outlier: 3.756A pdb=" N GLN 2 46 " --> pdb=" O ALA 2 42 " (cutoff:3.500A) Processing helix chain '6' and resid 19 through 24 removed outlier: 3.667A pdb=" N SER 6 24 " --> pdb=" O ARG 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 39 removed outlier: 3.758A pdb=" N VAL 6 31 " --> pdb=" O ASN 6 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU 6 32 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG 6 34 " --> pdb=" O LYS 6 30 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG 6 37 " --> pdb=" O ALA 6 33 " (cutoff:3.500A) Processing helix chain '9' and resid 3 through 7 removed outlier: 4.012A pdb=" N LEU 9 7 " --> pdb=" O GLN 9 4 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 17 removed outlier: 3.592A pdb=" N ASP 9 15 " --> pdb=" O VAL 9 11 " (cutoff:3.500A) Processing helix chain '9' and resid 46 through 62 removed outlier: 4.258A pdb=" N ALA 9 50 " --> pdb=" O ARG 9 46 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE 9 51 " --> pdb=" O GLN 9 47 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA 9 52 " --> pdb=" O VAL 9 48 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL 9 55 " --> pdb=" O ILE 9 51 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU 9 57 " --> pdb=" O ARG 9 53 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN 9 62 " --> pdb=" O VAL 9 58 " (cutoff:3.500A) Processing helix chain '9' and resid 93 through 99 Processing helix chain '9' and resid 99 through 104 removed outlier: 3.805A pdb=" N LEU 9 103 " --> pdb=" O ASN 9 99 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR 9 104 " --> pdb=" O ILE 9 100 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 99 through 104' Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'D' and resid 75 through 81 removed outlier: 4.782A pdb=" N VAL D 77 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 94 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER D 79 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 93 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 95 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.715A pdb=" N GLU D 116 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN D 127 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 162 through 163 removed outlier: 3.565A pdb=" N GLN D 162 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 4 through 16 removed outlier: 5.577A pdb=" N LYS E 9 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU E 29 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY E 11 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 27 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 197 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 194 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL E 188 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 196 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU E 184 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 116 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 212 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 38 removed outlier: 6.982A pdb=" N GLN E 50 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AA9, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.780A pdb=" N VAL F 154 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU F 153 " --> pdb=" O LEU F 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 16 through 20 Processing sheet with id=AB2, first strand: chain 'N' and resid 16 through 24 removed outlier: 7.022A pdb=" N ASN N 45 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL N 19 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL N 43 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR N 21 " --> pdb=" O CYS N 41 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS N 41 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS N 23 " --> pdb=" O ILE N 39 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE N 39 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL N 63 " --> pdb=" O ALA N 83 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 71 removed outlier: 3.698A pdb=" N SER N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR N 76 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR S 60 " --> pdb=" O ARG S 52 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG S 52 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR S 62 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE S 66 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N GLU S 46 " --> pdb=" O ILE S 66 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS S 85 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 76 through 78 removed outlier: 3.598A pdb=" N ILE O 111 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 32 through 34 removed outlier: 3.821A pdb=" N LEU P 34 " --> pdb=" O PHE P 104 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 41 through 43 removed outlier: 3.746A pdb=" N ILE P 42 " --> pdb=" O ALA P 95 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY P 92 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR P 72 " --> pdb=" O ILE P 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 29 through 33 removed outlier: 4.674A pdb=" N SER Q 116 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AB9, first strand: chain 'R' and resid 34 through 35 removed outlier: 4.055A pdb=" N TYR R 34 " --> pdb=" O TYR R 41 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR R 41 " --> pdb=" O TYR R 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 10 through 14 removed outlier: 3.696A pdb=" N ILE U 12 " --> pdb=" O ILE U 5 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU U 6 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL U 38 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 19 through 22 removed outlier: 3.816A pdb=" N ILE U 20 " --> pdb=" O LEU U 95 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE U 97 " --> pdb=" O THR U 61 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR U 61 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS U 99 " --> pdb=" O THR U 59 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 71 through 77 removed outlier: 3.678A pdb=" N VAL U 73 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS U 86 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR U 75 " --> pdb=" O ARG U 84 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG U 84 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER U 82 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 2 through 10 removed outlier: 5.519A pdb=" N LYS V 4 " --> pdb=" O VAL V 107 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL V 107 " --> pdb=" O LYS V 4 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL V 6 " --> pdb=" O ILE V 105 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE V 105 " --> pdb=" O VAL V 6 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ARG V 8 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE V 103 " --> pdb=" O ARG V 8 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS V 102 " --> pdb=" O ALA V 76 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA V 76 " --> pdb=" O HIS V 102 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR V 104 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA V 74 " --> pdb=" O THR V 104 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL V 106 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 82 through 87 Processing sheet with id=AC6, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.812A pdb=" N ASP W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE W 79 " --> pdb=" O VAL W 53 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL W 53 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR W 81 " --> pdb=" O ALA W 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'X' and resid 41 through 42 removed outlier: 4.072A pdb=" N MET X 41 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR X 59 " --> pdb=" O MET X 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'X' and resid 82 through 85 removed outlier: 3.676A pdb=" N ILE X 93 " --> pdb=" O GLY X 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 72 through 73 Processing sheet with id=AD2, first strand: chain 'Z' and resid 30 through 31 Processing sheet with id=AD3, first strand: chain 'Z' and resid 38 through 39 removed outlier: 3.637A pdb=" N GLY Z 73 " --> pdb=" O VAL Z 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 43 through 44 removed outlier: 3.706A pdb=" N SER Z 43 " --> pdb=" O ALA Z 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 53 through 55 removed outlier: 3.681A pdb=" N VAL Z 87 " --> pdb=" O TYR Z 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '0' and resid 13 through 14 removed outlier: 4.476A pdb=" N THR 0 14 " --> pdb=" O ARG 0 27 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG 0 27 " --> pdb=" O THR 0 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '2' and resid 3 through 7 removed outlier: 3.531A pdb=" N VAL 2 35 " --> pdb=" O ILE 2 6 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 15 through 16 Processing sheet with id=AD9, first strand: chain '9' and resid 78 through 81 removed outlier: 3.681A pdb=" N ILE 9 80 " --> pdb=" O VAL 9 87 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL 9 86 " --> pdb=" O TYR 9 36 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS 9 88 " --> pdb=" O VAL 9 38 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 909 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 827 hydrogen bonds 1324 hydrogen bond angles 0 basepair planarities 373 basepair parallelities 1309 stacking parallelities Total time for adding SS restraints: 99.98 Time building geometry restraints manager: 16.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11455 1.33 - 1.45: 36750 1.45 - 1.57: 31746 1.57 - 1.70: 5368 1.70 - 1.82: 89 Bond restraints: 85408 Sorted by residual: bond pdb=" CA ARG D 174 " pdb=" CB ARG D 174 " ideal model delta sigma weight residual 1.526 1.429 0.097 1.76e-02 3.23e+03 3.04e+01 bond pdb=" C1' U A 99 " pdb=" N1 U A 99 " ideal model delta sigma weight residual 1.480 1.557 -0.077 1.50e-02 4.44e+03 2.64e+01 bond pdb=" N PRO D 147 " pdb=" CD PRO D 147 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" CB THR 4 18 " pdb=" CG2 THR 4 18 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CG ARG O 33 " pdb=" CD ARG O 33 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.84e+00 ... (remaining 85403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 125625 2.81 - 5.62: 2786 5.62 - 8.43: 171 8.43 - 11.24: 13 11.24 - 14.05: 1 Bond angle restraints: 128596 Sorted by residual: angle pdb=" CA GLY R 103 " pdb=" C GLY R 103 " pdb=" N ARG R 104 " ideal model delta sigma weight residual 115.43 120.93 -5.50 9.80e-01 1.04e+00 3.15e+01 angle pdb=" C3' U A 661 " pdb=" O3' U A 661 " pdb=" P G A 662 " ideal model delta sigma weight residual 120.20 127.80 -7.60 1.50e+00 4.44e-01 2.57e+01 angle pdb=" C4' U A1750 " pdb=" C3' U A1750 " pdb=" O3' U A1750 " ideal model delta sigma weight residual 109.40 116.26 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" CA GLY R 103 " pdb=" C GLY R 103 " pdb=" O GLY R 103 " ideal model delta sigma weight residual 121.77 117.84 3.93 8.60e-01 1.35e+00 2.08e+01 angle pdb=" N ILE E 215 " pdb=" CA ILE E 215 " pdb=" C ILE E 215 " ideal model delta sigma weight residual 112.96 108.51 4.45 1.00e+00 1.00e+00 1.98e+01 ... (remaining 128591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 47642 35.53 - 71.07: 6143 71.07 - 106.60: 755 106.60 - 142.14: 26 142.14 - 177.67: 14 Dihedral angle restraints: 54580 sinusoidal: 47170 harmonic: 7410 Sorted by residual: dihedral pdb=" O4' U B 100 " pdb=" C1' U B 100 " pdb=" N1 U B 100 " pdb=" C2 U B 100 " ideal model delta sinusoidal sigma weight residual 200.00 22.92 177.08 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2384 " pdb=" C1' U A2384 " pdb=" N1 U A2384 " pdb=" C2 U A2384 " ideal model delta sinusoidal sigma weight residual 200.00 24.96 175.04 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A1932 " pdb=" C1' C A1932 " pdb=" N1 C A1932 " pdb=" C2 C A1932 " ideal model delta sinusoidal sigma weight residual 200.00 26.63 173.37 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 54577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 12565 0.062 - 0.124: 3385 0.124 - 0.186: 545 0.186 - 0.249: 77 0.249 - 0.311: 8 Chirality restraints: 16580 Sorted by residual: chirality pdb=" CG LEU U 25 " pdb=" CB LEU U 25 " pdb=" CD1 LEU U 25 " pdb=" CD2 LEU U 25 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' A A 700 " pdb=" C4' A A 700 " pdb=" O3' A A 700 " pdb=" C2' A A 700 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' A A 353 " pdb=" O4' A A 353 " pdb=" C2' A A 353 " pdb=" N9 A A 353 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 16577 not shown) Planarity restraints: 6256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 700 " 0.036 2.00e-02 2.50e+03 1.89e-02 9.81e+00 pdb=" N9 A A 700 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A A 700 " -0.011 2.00e-02 2.50e+03 pdb=" N7 A A 700 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 700 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A 700 " -0.028 2.00e-02 2.50e+03 pdb=" N6 A A 700 " 0.031 2.00e-02 2.50e+03 pdb=" N1 A A 700 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A 700 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 700 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A A 700 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 557 " 0.038 2.00e-02 2.50e+03 1.74e-02 9.12e+00 pdb=" N9 G A 557 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G A 557 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 557 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 557 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A 557 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G A 557 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A 557 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A 557 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G A 557 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 557 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 557 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 845 " -0.035 2.00e-02 2.50e+03 1.71e-02 8.05e+00 pdb=" N9 A A 845 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A A 845 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A A 845 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A 845 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 845 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 845 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A A 845 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 845 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 845 " -0.001 2.00e-02 2.50e+03 pdb=" C4 A A 845 " -0.001 2.00e-02 2.50e+03 ... (remaining 6253 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.54: 667 2.54 - 3.19: 62616 3.19 - 3.84: 158154 3.84 - 4.49: 240038 4.49 - 5.14: 324755 Nonbonded interactions: 786230 Sorted by model distance: nonbonded pdb=" O PRO O 48 " pdb=" NZ LYS 7 59 " model vdw 1.886 3.120 nonbonded pdb=" OP2 C A1352 " pdb="MG MG A3006 " model vdw 1.900 2.170 nonbonded pdb=" O2 C A 674 " pdb=" O2' U A 684 " model vdw 1.935 3.040 nonbonded pdb=" OP1 U A2642 " pdb="MG MG A3023 " model vdw 1.961 2.170 nonbonded pdb=" OP1 G A1369 " pdb="MG MG A3006 " model vdw 1.962 2.170 ... (remaining 786225 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=0.00 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.430 Check model and map are aligned: 0.470 Set scattering table: 0.550 Process input model: 214.940 Find NCS groups from input model: 0.970 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: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.010 0.140 85408 Z= 0.621 Angle : 1.052 14.052 128596 Z= 0.524 Chirality : 0.057 0.311 16580 Planarity : 0.006 0.067 6256 Dihedral : 23.892 177.673 49812 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.67 % Favored : 82.18 % Rotamer: Outliers : 0.14 % Allowed : 2.85 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -6.09 (0.11), residues: 2553 helix: -4.89 (0.10), residues: 507 sheet: -3.52 (0.21), residues: 353 loop : -4.17 (0.11), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP 9 77 HIS 0.025 0.004 HIS X 44 PHE 0.036 0.004 PHE Q 86 TYR 0.044 0.005 TYR F 99 ARG 0.021 0.003 ARG O 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 519 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 141 ASN cc_start: 0.8030 (m-40) cc_final: 0.7771 (m-40) REVERT: M 20 ASP cc_start: 0.6982 (t70) cc_final: 0.6618 (t0) REVERT: N 57 VAL cc_start: 0.8381 (m) cc_final: 0.8143 (t) REVERT: O 13 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7237 (mtt90) REVERT: P 5 LYS cc_start: 0.7565 (mttp) cc_final: 0.7247 (mtmt) REVERT: Z 35 ASP cc_start: 0.6500 (t0) cc_final: 0.6155 (t0) outliers start: 3 outliers final: 0 residues processed: 522 average time/residue: 0.8568 time to fit residues: 729.4763 Evaluate side-chains 367 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 6.9990 chunk 394 optimal weight: 0.0040 chunk 218 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 407 optimal weight: 0.4980 chunk 157 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 303 optimal weight: 0.7980 chunk 472 optimal weight: 0.0870 overall best weight: 1.6772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS D 85 ASN D 127 ASN D 142 ASN D 198 GLN E 19 ASN E 76 HIS E 143 HIS E 182 ASN F 182 ASN M 81 HIS Q 97 GLN R 15 HIS S 31 HIS T 37 GLN U 18 GLN U 28 ASN V 61 ASN V 77 ASN X 39 ASN X 51 ASN Y 84 ASN Y 88 HIS Z 58 ASN 7 7 HIS 7 43 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 85408 Z= 0.175 Angle : 0.706 9.791 128596 Z= 0.358 Chirality : 0.039 0.271 16580 Planarity : 0.005 0.060 6256 Dihedral : 24.223 177.455 44564 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.56 % Allowed : 7.86 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -5.08 (0.13), residues: 2553 helix: -3.92 (0.15), residues: 533 sheet: -2.76 (0.22), residues: 432 loop : -3.54 (0.12), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 9 77 HIS 0.012 0.001 HIS R 15 PHE 0.015 0.002 PHE T 57 TYR 0.015 0.001 TYR R 101 ARG 0.006 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 414 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 3 LYS cc_start: 0.7670 (ptpt) cc_final: 0.7233 (mmtt) REVERT: F 107 ARG cc_start: 0.7014 (ttp-170) cc_final: 0.6803 (ttm170) REVERT: F 110 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (tt) REVERT: N 94 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7498 (ttm-80) REVERT: O 13 ARG cc_start: 0.7677 (mmt90) cc_final: 0.7312 (mtt-85) REVERT: P 5 LYS cc_start: 0.7587 (mttp) cc_final: 0.7273 (mtmt) REVERT: P 54 MET cc_start: 0.6889 (ttt) cc_final: 0.6631 (ttm) REVERT: V 62 TYR cc_start: 0.6653 (m-80) cc_final: 0.6413 (m-80) REVERT: 9 91 HIS cc_start: 0.5414 (t-90) cc_final: 0.5136 (t70) outliers start: 34 outliers final: 19 residues processed: 430 average time/residue: 0.7988 time to fit residues: 576.0618 Evaluate side-chains 379 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 359 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 7 residue 56 LYS Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 393 optimal weight: 0.1980 chunk 321 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 473 optimal weight: 0.7980 chunk 511 optimal weight: 3.9990 chunk 421 optimal weight: 0.8980 chunk 469 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN F 188 ASN ** R 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 GLN U 28 ASN V 61 ASN X 44 HIS Y 84 ASN Z 58 ASN 7 43 GLN 7 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 85408 Z= 0.137 Angle : 0.581 10.270 128596 Z= 0.299 Chirality : 0.034 0.283 16580 Planarity : 0.004 0.046 6256 Dihedral : 23.878 175.135 44564 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.25 % Allowed : 11.12 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.14), residues: 2553 helix: -2.88 (0.19), residues: 533 sheet: -2.08 (0.23), residues: 461 loop : -3.22 (0.13), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 77 HIS 0.006 0.001 HIS X 44 PHE 0.011 0.001 PHE O 85 TYR 0.022 0.001 TYR N 76 ARG 0.006 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 410 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 114 ASN cc_start: 0.6868 (t0) cc_final: 0.6539 (t0) REVERT: P 5 LYS cc_start: 0.7592 (mttp) cc_final: 0.7269 (mtpt) REVERT: Z 52 LYS cc_start: 0.7379 (mptt) cc_final: 0.6876 (mtmm) REVERT: Z 68 PHE cc_start: 0.7436 (p90) cc_final: 0.7180 (p90) REVERT: Z 76 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7726 (mtpp) REVERT: Z 84 LYS cc_start: 0.7186 (ttmm) cc_final: 0.6807 (ttmm) REVERT: 9 91 HIS cc_start: 0.5344 (t-90) cc_final: 0.5105 (t70) outliers start: 49 outliers final: 29 residues processed: 433 average time/residue: 0.8487 time to fit residues: 610.9626 Evaluate side-chains 385 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 356 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 94 MET Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain X residue 33 VAL Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 7 residue 56 LYS Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 2.9990 chunk 355 optimal weight: 8.9990 chunk 245 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 502 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 449 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN O 27 ASN O 143 HIS P 25 ASN ** R 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 HIS T 44 GLN U 18 GLN U 63 ASN V 61 ASN V 77 ASN Y 84 ASN Z 58 ASN 0 23 ASN 1 64 GLN 7 43 GLN 9 88 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 85408 Z= 0.426 Angle : 0.899 13.273 128596 Z= 0.442 Chirality : 0.047 0.308 16580 Planarity : 0.007 0.070 6256 Dihedral : 24.206 176.544 44564 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 3.77 % Allowed : 14.48 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.43 (0.14), residues: 2553 helix: -3.24 (0.17), residues: 549 sheet: -1.94 (0.24), residues: 427 loop : -3.29 (0.12), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 9 77 HIS 0.012 0.002 HIS D 57 PHE 0.024 0.003 PHE E 91 TYR 0.029 0.003 TYR F 99 ARG 0.007 0.001 ARG S 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 375 time to evaluate : 3.305 Fit side-chains revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7357 (mp) REVERT: D 182 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.5206 (mmm) REVERT: M 118 LYS cc_start: 0.7495 (tptp) cc_final: 0.7166 (ttmt) REVERT: S 87 GLU cc_start: 0.7790 (mp0) cc_final: 0.7493 (mp0) REVERT: Z 52 LYS cc_start: 0.7592 (mptt) cc_final: 0.7185 (mttp) REVERT: Z 68 PHE cc_start: 0.7554 (p90) cc_final: 0.7287 (p90) REVERT: Z 84 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7043 (ttmm) outliers start: 82 outliers final: 60 residues processed: 432 average time/residue: 0.8083 time to fit residues: 590.4310 Evaluate side-chains 406 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 344 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain P residue 129 THR Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 374 optimal weight: 0.5980 chunk 207 optimal weight: 20.0000 chunk 428 optimal weight: 0.5980 chunk 347 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 overall best weight: 3.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 HIS E 19 ASN Q 61 ASN ** R 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN 0 23 ASN 7 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 85408 Z= 0.191 Angle : 0.641 10.336 128596 Z= 0.329 Chirality : 0.037 0.285 16580 Planarity : 0.005 0.047 6256 Dihedral : 23.911 174.997 44564 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.22 % Allowed : 16.18 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.14), residues: 2553 helix: -2.78 (0.19), residues: 543 sheet: -1.77 (0.25), residues: 439 loop : -3.12 (0.12), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 212 HIS 0.007 0.001 HIS O 143 PHE 0.014 0.001 PHE T 106 TYR 0.025 0.002 TYR N 76 ARG 0.008 0.001 ARG 9 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 365 time to evaluate : 3.182 Fit side-chains revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7267 (mp) REVERT: D 182 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5024 (mmm) REVERT: F 40 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7862 (tp40) REVERT: N 2 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7395 (mp) REVERT: S 87 GLU cc_start: 0.7819 (mp0) cc_final: 0.7505 (mp0) REVERT: Z 52 LYS cc_start: 0.7554 (mptt) cc_final: 0.7000 (mtmm) REVERT: Z 68 PHE cc_start: 0.7583 (p90) cc_final: 0.7332 (p90) REVERT: Z 84 LYS cc_start: 0.7378 (ttmm) cc_final: 0.6965 (ttmm) REVERT: 1 8 ASP cc_start: 0.5792 (m-30) cc_final: 0.5390 (p0) outliers start: 70 outliers final: 50 residues processed: 409 average time/residue: 0.7961 time to fit residues: 552.3347 Evaluate side-chains 399 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 345 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 40 GLN Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 30.0000 chunk 452 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 503 optimal weight: 9.9990 chunk 417 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 264 optimal weight: 30.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 HIS Q 61 ASN ** R 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN 0 23 ASN 7 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 85408 Z= 0.439 Angle : 0.926 14.250 128596 Z= 0.456 Chirality : 0.049 0.329 16580 Planarity : 0.006 0.059 6256 Dihedral : 24.262 176.960 44564 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 4.78 % Allowed : 16.64 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.14), residues: 2553 helix: -3.18 (0.17), residues: 555 sheet: -2.03 (0.23), residues: 462 loop : -3.21 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 212 HIS 0.011 0.002 HIS D 57 PHE 0.026 0.003 PHE E 91 TYR 0.031 0.003 TYR N 76 ARG 0.009 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 340 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7423 (mp) REVERT: D 182 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.4966 (mmm) REVERT: E 88 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8103 (mm) REVERT: F 40 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7244 (tp40) REVERT: M 118 LYS cc_start: 0.7509 (tptp) cc_final: 0.7229 (ttmt) REVERT: N 2 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7387 (mp) REVERT: P 72 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.5968 (p) REVERT: S 87 GLU cc_start: 0.7918 (mp0) cc_final: 0.7601 (mp0) REVERT: T 19 LYS cc_start: 0.8042 (tptt) cc_final: 0.7499 (tptp) REVERT: V 68 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7261 (tm-30) REVERT: Z 52 LYS cc_start: 0.7785 (mptt) cc_final: 0.7467 (mttp) REVERT: Z 68 PHE cc_start: 0.7780 (p90) cc_final: 0.7530 (p90) REVERT: Z 84 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7178 (ttmm) outliers start: 104 outliers final: 81 residues processed: 416 average time/residue: 0.7958 time to fit residues: 561.9368 Evaluate side-chains 414 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 327 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 193 LYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 40 GLN Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 59 THR Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 78 GLU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 8 THR Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 7 residue 58 VAL Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 367 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 423 optimal weight: 0.9990 chunk 280 optimal weight: 7.9990 chunk 501 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 ASN ** R 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN V 60 HIS W 57 ASN ** X 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 23 ASN 7 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 85408 Z= 0.174 Angle : 0.631 10.463 128596 Z= 0.325 Chirality : 0.037 0.287 16580 Planarity : 0.004 0.049 6256 Dihedral : 23.897 175.919 44564 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.63 % Allowed : 18.70 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.92 (0.14), residues: 2553 helix: -2.64 (0.19), residues: 552 sheet: -1.62 (0.25), residues: 429 loop : -3.04 (0.13), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 212 HIS 0.012 0.001 HIS V 60 PHE 0.015 0.001 PHE T 106 TYR 0.027 0.002 TYR N 76 ARG 0.007 0.000 ARG N 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 362 time to evaluate : 3.190 Fit side-chains revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7254 (mp) REVERT: D 182 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.4929 (mmm) REVERT: E 14 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6044 (pm20) REVERT: S 75 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7503 (p) REVERT: S 87 GLU cc_start: 0.7851 (mp0) cc_final: 0.7554 (mp0) REVERT: T 74 MET cc_start: 0.5209 (mtm) cc_final: 0.5005 (mmp) REVERT: Y 73 MET cc_start: 0.4508 (mpp) cc_final: 0.4293 (mpp) REVERT: Y 87 THR cc_start: 0.1360 (OUTLIER) cc_final: 0.1037 (p) REVERT: Z 52 LYS cc_start: 0.7691 (mptt) cc_final: 0.7389 (mttp) REVERT: Z 68 PHE cc_start: 0.7760 (p90) cc_final: 0.7548 (p90) REVERT: Z 84 LYS cc_start: 0.7588 (ttmm) cc_final: 0.7130 (ttmm) outliers start: 79 outliers final: 54 residues processed: 415 average time/residue: 0.7865 time to fit residues: 554.5190 Evaluate side-chains 403 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 344 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 2 GLU Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 HIS Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain Y residue 87 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 299 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 318 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 393 optimal weight: 0.9980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN U 18 GLN V 60 HIS ** X 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 85408 Z= 0.273 Angle : 0.712 10.418 128596 Z= 0.360 Chirality : 0.040 0.289 16580 Planarity : 0.005 0.048 6256 Dihedral : 23.922 174.878 44564 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 3.91 % Allowed : 18.61 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.92 (0.14), residues: 2553 helix: -2.68 (0.19), residues: 565 sheet: -1.66 (0.24), residues: 441 loop : -3.00 (0.13), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 212 HIS 0.013 0.002 HIS V 60 PHE 0.016 0.002 PHE E 91 TYR 0.028 0.002 TYR N 76 ARG 0.004 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 340 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7405 (mp) REVERT: D 175 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6871 (pp) REVERT: D 182 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.4959 (mmm) REVERT: E 14 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: F 7 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6247 (tp) REVERT: F 40 GLN cc_start: 0.7968 (tp40) cc_final: 0.7723 (tp40) REVERT: N 91 LYS cc_start: 0.6647 (mmtt) cc_final: 0.6341 (ptpp) REVERT: P 5 LYS cc_start: 0.7799 (mttp) cc_final: 0.7379 (mtpt) REVERT: P 72 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.6026 (p) REVERT: Y 73 MET cc_start: 0.4574 (mpp) cc_final: 0.4174 (mpp) REVERT: Y 87 THR cc_start: 0.1558 (OUTLIER) cc_final: 0.1223 (p) REVERT: Z 52 LYS cc_start: 0.7769 (mptt) cc_final: 0.7473 (mttp) REVERT: Z 84 LYS cc_start: 0.7634 (ttmm) cc_final: 0.7086 (ttmm) REVERT: 9 41 HIS cc_start: 0.5629 (p90) cc_final: 0.5102 (p90) outliers start: 85 outliers final: 68 residues processed: 401 average time/residue: 0.8015 time to fit residues: 544.6901 Evaluate side-chains 411 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 336 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 7 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 83 ILE Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 60 HIS Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 87 THR Chi-restraints excluded: chain Y residue 96 MET Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 66 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 1.9990 chunk 480 optimal weight: 8.9990 chunk 438 optimal weight: 2.9990 chunk 467 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 366 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 422 optimal weight: 3.9990 chunk 441 optimal weight: 9.9990 chunk 465 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN V 60 HIS ** X 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 85408 Z= 0.201 Angle : 0.652 12.754 128596 Z= 0.336 Chirality : 0.038 0.287 16580 Planarity : 0.005 0.049 6256 Dihedral : 23.894 174.599 44564 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.81 % Allowed : 18.84 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.81 (0.14), residues: 2553 helix: -2.60 (0.19), residues: 571 sheet: -1.51 (0.25), residues: 432 loop : -2.95 (0.13), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 212 HIS 0.007 0.001 HIS V 60 PHE 0.015 0.002 PHE T 106 TYR 0.027 0.002 TYR N 76 ARG 0.005 0.000 ARG N 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 339 time to evaluate : 3.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 175 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6850 (pp) REVERT: D 182 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.4956 (mmm) REVERT: E 14 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: F 7 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6202 (tp) REVERT: N 91 LYS cc_start: 0.6594 (mmtt) cc_final: 0.6346 (ptpp) REVERT: P 72 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.6032 (p) REVERT: Y 73 MET cc_start: 0.4530 (mpp) cc_final: 0.4150 (mpp) REVERT: Y 87 THR cc_start: 0.1540 (OUTLIER) cc_final: 0.1212 (p) REVERT: Z 52 LYS cc_start: 0.7735 (mptt) cc_final: 0.7217 (mtmm) REVERT: Z 84 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7089 (ttmm) REVERT: 9 41 HIS cc_start: 0.5596 (p90) cc_final: 0.5074 (p90) outliers start: 83 outliers final: 69 residues processed: 401 average time/residue: 0.8026 time to fit residues: 547.4626 Evaluate side-chains 409 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 333 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 193 LYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 27 SER Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 87 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.0980 chunk 493 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 518 optimal weight: 7.9990 chunk 476 optimal weight: 8.9990 chunk 412 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN V 60 HIS ** X 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 85408 Z= 0.178 Angle : 0.626 10.352 128596 Z= 0.323 Chirality : 0.036 0.285 16580 Planarity : 0.005 0.067 6256 Dihedral : 23.846 174.069 44564 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 3.77 % Allowed : 19.12 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.70 (0.14), residues: 2553 helix: -2.46 (0.19), residues: 571 sheet: -1.45 (0.25), residues: 427 loop : -2.89 (0.13), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 212 HIS 0.013 0.001 HIS V 60 PHE 0.016 0.001 PHE T 106 TYR 0.026 0.002 TYR N 76 ARG 0.006 0.000 ARG N 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5106 Ramachandran restraints generated. 2553 Oldfield, 0 Emsley, 2553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 345 time to evaluate : 3.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7367 (mp) REVERT: D 101 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6489 (mtt180) REVERT: D 175 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6820 (pp) REVERT: D 182 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.4932 (mmm) REVERT: E 14 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6149 (pm20) REVERT: N 2 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7407 (mp) REVERT: N 94 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7609 (ttm-80) REVERT: P 5 LYS cc_start: 0.7838 (mttp) cc_final: 0.7454 (mtpt) REVERT: P 72 THR cc_start: 0.6280 (OUTLIER) cc_final: 0.5990 (p) REVERT: S 75 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7484 (p) REVERT: T 19 LYS cc_start: 0.8070 (tptt) cc_final: 0.7781 (tptp) REVERT: Y 73 MET cc_start: 0.4531 (mpp) cc_final: 0.4197 (mpp) REVERT: Y 87 THR cc_start: 0.1516 (OUTLIER) cc_final: 0.1204 (p) REVERT: Z 52 LYS cc_start: 0.7699 (mptt) cc_final: 0.7188 (mtmm) REVERT: Z 84 LYS cc_start: 0.7591 (ttmm) cc_final: 0.7047 (ttmm) REVERT: 9 41 HIS cc_start: 0.5573 (p90) cc_final: 0.5075 (p90) outliers start: 82 outliers final: 68 residues processed: 405 average time/residue: 0.8017 time to fit residues: 551.9883 Evaluate side-chains 417 residues out of total 2180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 340 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 101 ARG Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain E residue 193 LYS Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 65 THR Chi-restraints excluded: chain N residue 76 TYR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 92 THR Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 72 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 10 THR Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 94 SER Chi-restraints excluded: chain W residue 14 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 4 LYS Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 87 THR Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain 2 residue 34 SER Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 7 residue 32 LEU Chi-restraints excluded: chain 9 residue 39 VAL Chi-restraints excluded: chain 9 residue 87 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 3.9990 chunk 439 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 413 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 424 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 10.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** X 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.151656 restraints weight = 125739.134| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 0.80 r_work: 0.3619 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 85408 Z= 0.291 Angle : 0.727 11.560 128596 Z= 0.367 Chirality : 0.041 0.282 16580 Planarity : 0.005 0.048 6256 Dihedral : 23.925 173.568 44564 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 4.04 % Allowed : 19.21 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.81 (0.14), residues: 2553 helix: -2.53 (0.19), residues: 559 sheet: -1.53 (0.25), residues: 434 loop : -2.97 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 212 HIS 0.007 0.002 HIS V 102 PHE 0.015 0.002 PHE T 106 TYR 0.028 0.002 TYR N 76 ARG 0.005 0.001 ARG E 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12115.16 seconds wall clock time: 213 minutes 22.05 seconds (12802.05 seconds total)