Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 02:26:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppf_20435/04_2023/6ppf_20435.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2583 5.49 5 S 49 5.16 5 C 34973 2.51 5 N 13376 2.21 5 O 20854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E GLU 138": "OE1" <-> "OE2" Residue "J ARG 94": "NH1" <-> "NH2" Residue "J TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P GLU 74": "OE1" <-> "OE2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U ARG 92": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "Y GLU 15": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 71835 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 53094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2471, 53094 Classifications: {'RNA': 2471} Modifications used: {'rna2p_pur': 236, 'rna2p_pyr': 129, 'rna3p_pur': 1213, 'rna3p_pyr': 893} Link IDs: {'rna2p': 365, 'rna3p': 2105} Chain breaks: 12 Chain: "B" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 45} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1684 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "D" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1265 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain breaks: 2 Chain: "E" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1484 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 2 Chain: "J" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1119 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 8, 'TRANS': 132} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 952 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain breaks: 1 Chain: "P" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 846 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "U" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 739 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 555 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 28.17, per 1000 atoms: 0.39 Number of scatterers: 71835 At special positions: 0 Unit cell: (203.87, 196.359, 219.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 2583 15.00 O 20854 8.00 N 13376 7.00 C 34973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.20 Conformation dependent library (CDL) restraints added in 2.6 seconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 36 sheets defined 27.1% alpha, 15.7% beta 681 base pairs and 1275 stacking pairs defined. Time for finding SS restraints: 23.63 Creating SS restraints... Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.764A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 201' Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.646A pdb=" N ILE D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.528A pdb=" N LEU E 38 " --> pdb=" O PHE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.847A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 147 removed outlier: 3.517A pdb=" N LYS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.535A pdb=" N VAL E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 206 removed outlier: 4.144A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 31 Processing helix chain 'J' and resid 32 through 38 removed outlier: 3.708A pdb=" N ILE J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 72 Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.065A pdb=" N MET J 101 " --> pdb=" O TYR J 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.798A pdb=" N LEU K 106 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 108 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 removed outlier: 3.708A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.807A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY L 26 " --> pdb=" O ILE L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 22 through 26' Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.602A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 140 removed outlier: 3.668A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 4.594A pdb=" N ASP N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 41 removed outlier: 3.616A pdb=" N GLU N 39 " --> pdb=" O THR N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 4.300A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 3.799A pdb=" N GLN N 61 " --> pdb=" O HIS N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 86 Processing helix chain 'N' and resid 87 through 90 Processing helix chain 'O' and resid 7 through 22 removed outlier: 3.592A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 78 removed outlier: 3.564A pdb=" N VAL O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 86 removed outlier: 3.696A pdb=" N LYS O 83 " --> pdb=" O GLU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 115 Processing helix chain 'P' and resid 6 through 12 Processing helix chain 'P' and resid 100 through 105 removed outlier: 3.719A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU P 105 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 21 removed outlier: 4.153A pdb=" N LYS Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG Q 13 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.867A pdb=" N HIS Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 69 removed outlier: 4.164A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET Q 40 " --> pdb=" O ASN Q 36 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS Q 41 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 48 " --> pdb=" O ASN Q 44 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA Q 67 " --> pdb=" O THR Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 73 removed outlier: 3.546A pdb=" N GLY Q 73 " --> pdb=" O ARG Q 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 70 through 73' Processing helix chain 'Q' and resid 76 through 81 Processing helix chain 'Q' and resid 92 through 97 Processing helix chain 'Q' and resid 103 through 118 removed outlier: 4.154A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA Q 110 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA Q 112 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 Processing helix chain 'S' and resid 29 through 38 removed outlier: 4.169A pdb=" N SER S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 62 removed outlier: 3.665A pdb=" N ILE S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL S 50 " --> pdb=" O ILE S 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA S 56 " --> pdb=" O LYS S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'T' and resid 4 through 7 No H-bonds generated for 'chain 'T' and resid 4 through 7' Processing helix chain 'T' and resid 14 through 21 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.991A pdb=" N VAL T 39 " --> pdb=" O ASN T 35 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER T 45 " --> pdb=" O ASP T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 17 removed outlier: 4.194A pdb=" N ASP U 16 " --> pdb=" O SER U 13 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS U 17 " --> pdb=" O GLY U 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 13 through 17' Processing helix chain 'Z' and resid 16 through 26 removed outlier: 3.574A pdb=" N ARG Z 20 " --> pdb=" O PRO Z 16 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Z 21 " --> pdb=" O GLU Z 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL Z 23 " --> pdb=" O GLN Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.608A pdb=" N ARG Z 44 " --> pdb=" O ASN Z 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 15 Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.617A pdb=" N ILE Y 6 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 15 removed outlier: 3.575A pdb=" N GLU Y 15 " --> pdb=" O THR Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 32 removed outlier: 3.589A pdb=" N GLU Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 54 removed outlier: 3.854A pdb=" N LYS Y 48 " --> pdb=" O ARG Y 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA Y 49 " --> pdb=" O GLU Y 45 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 64 removed outlier: 3.684A pdb=" N ILE Y 62 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.811A pdb=" N ARG d 28 " --> pdb=" O SER d 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU d 29 " --> pdb=" O LYS d 25 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.938A pdb=" N THR C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.577A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'C' and resid 163 through 167 removed outlier: 4.499A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS C 167 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.576A pdb=" N VAL D 108 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN D 173 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.809A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 27 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 188 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 28 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 186 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 15 through 16 removed outlier: 4.099A pdb=" N VAL D 15 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE D 23 " --> pdb=" O VAL D 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 37 through 39 removed outlier: 3.681A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 120 Processing sheet with id=AB2, first strand: chain 'E' and resid 6 through 7 removed outlier: 6.140A pdb=" N ILE E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 123 through 125 removed outlier: 7.435A pdb=" N TRP J 16 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'K' and resid 8 through 10 removed outlier: 7.020A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS K 59 " --> pdb=" O ILE K 87 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.944A pdb=" N ILE K 77 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.463A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS L 127 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE L 111 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.476A pdb=" N VAL L 123 " --> pdb=" O GLU L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 33 removed outlier: 3.563A pdb=" N THR N 32 " --> pdb=" O ALA N 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 70 through 72 removed outlier: 6.998A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 55 through 57 Processing sheet with id=AC3, first strand: chain 'P' and resid 71 through 73 Processing sheet with id=AC4, first strand: chain 'P' and resid 71 through 73 removed outlier: 3.821A pdb=" N THR P 63 " --> pdb=" O LYS P 52 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS P 52 " --> pdb=" O THR P 63 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG P 65 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL P 50 " --> pdb=" O ARG P 65 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ILE P 67 " --> pdb=" O GLY P 48 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY P 48 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR P 28 " --> pdb=" O VAL P 89 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL P 89 " --> pdb=" O THR P 28 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG P 30 " --> pdb=" O ILE P 87 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE P 87 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS P 32 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.141A pdb=" N THR R 96 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL R 62 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU R 98 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA R 60 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE R 100 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL R 58 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 58 " --> pdb=" O PHE R 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 73 through 75 Processing sheet with id=AC7, first strand: chain 'S' and resid 5 through 6 removed outlier: 6.893A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AD1, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.724A pdb=" N GLU T 29 " --> pdb=" O LYS T 9 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR T 27 " --> pdb=" O PRO T 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 20 through 21 Processing sheet with id=AD3, first strand: chain 'U' and resid 23 through 27 removed outlier: 6.984A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA U 26 " --> pdb=" O ARG U 32 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AD5, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AD6, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.921A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG V 47 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 73 through 79 removed outlier: 3.545A pdb=" N SER V 88 " --> pdb=" O LYS V 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 34 through 37 removed outlier: 3.504A pdb=" N THR Z 7 " --> pdb=" O SER Z 55 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'b' and resid 27 through 29 392 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1637 hydrogen bonds 2692 hydrogen bond angles 0 basepair planarities 681 basepair parallelities 1275 stacking parallelities Total time for adding SS restraints: 85.61 Time building geometry restraints manager: 34.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7677 1.32 - 1.44: 35394 1.44 - 1.56: 30356 1.56 - 1.69: 5152 1.69 - 1.81: 91 Bond restraints: 78670 Sorted by residual: bond pdb=" C ARG E 79 " pdb=" N SER E 80 " ideal model delta sigma weight residual 1.329 1.268 0.060 1.86e-02 2.89e+03 1.06e+01 bond pdb=" C HIS J 41 " pdb=" N LYS J 42 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.07e-02 2.33e+03 5.77e+00 bond pdb=" C3' U A1107 " pdb=" O3' U A1107 " ideal model delta sigma weight residual 1.427 1.457 -0.030 1.50e-02 4.44e+03 3.98e+00 bond pdb=" C5 A A1291 " pdb=" C6 A A1291 " ideal model delta sigma weight residual 1.406 1.368 0.038 2.00e-02 2.50e+03 3.57e+00 bond pdb=" C THR J 4 " pdb=" N PRO J 5 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.49e+00 ... (remaining 78665 not shown) Histogram of bond angle deviations from ideal: 85.95 - 96.70: 10 96.70 - 107.46: 18409 107.46 - 118.21: 58230 118.21 - 128.97: 40276 128.97 - 139.72: 2129 Bond angle restraints: 119054 Sorted by residual: angle pdb=" C LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta sigma weight residual 110.90 139.72 -28.82 1.58e+00 4.01e-01 3.33e+02 angle pdb=" C ILE O 90 " pdb=" CA ILE O 90 " pdb=" CB ILE O 90 " ideal model delta sigma weight residual 111.29 87.14 24.15 1.64e+00 3.72e-01 2.17e+02 angle pdb=" N ARG E 84 " pdb=" CA ARG E 84 " pdb=" C ARG E 84 " ideal model delta sigma weight residual 111.69 128.33 -16.64 1.23e+00 6.61e-01 1.83e+02 angle pdb=" C ILE R 22 " pdb=" CA ILE R 22 " pdb=" CB ILE R 22 " ideal model delta sigma weight residual 110.91 92.04 18.87 1.46e+00 4.69e-01 1.67e+02 angle pdb=" C PHE L 85 " pdb=" CA PHE L 85 " pdb=" CB PHE L 85 " ideal model delta sigma weight residual 109.33 85.95 23.38 1.97e+00 2.58e-01 1.41e+02 ... (remaining 119049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 38388 35.98 - 71.95: 2583 71.95 - 107.93: 204 107.93 - 143.91: 33 143.91 - 179.88: 49 Dihedral angle restraints: 41257 sinusoidal: 35306 harmonic: 5951 Sorted by residual: dihedral pdb=" C LEU Q 103 " pdb=" N LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta harmonic sigma weight residual -122.60 -163.99 41.39 0 2.50e+00 1.60e-01 2.74e+02 dihedral pdb=" N LEU Q 103 " pdb=" C LEU Q 103 " pdb=" CA LEU Q 103 " pdb=" CB LEU Q 103 " ideal model delta harmonic sigma weight residual 122.80 156.45 -33.65 0 2.50e+00 1.60e-01 1.81e+02 dihedral pdb=" C LYS D 56 " pdb=" N LYS D 56 " pdb=" CA LYS D 56 " pdb=" CB LYS D 56 " ideal model delta harmonic sigma weight residual -122.60 -92.06 -30.54 0 2.50e+00 1.60e-01 1.49e+02 ... (remaining 41254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 15406 0.334 - 0.667: 23 0.667 - 1.001: 2 1.001 - 1.334: 1 1.334 - 1.668: 1 Chirality restraints: 15433 Sorted by residual: chirality pdb=" CA LEU Q 103 " pdb=" N LEU Q 103 " pdb=" C LEU Q 103 " pdb=" CB LEU Q 103 " both_signs ideal model delta sigma weight residual False 2.51 0.84 1.67 2.00e-01 2.50e+01 6.95e+01 chirality pdb=" CA ALA J 60 " pdb=" N ALA J 60 " pdb=" C ALA J 60 " pdb=" CB ALA J 60 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CA ILE R 22 " pdb=" N ILE R 22 " pdb=" C ILE R 22 " pdb=" CB ILE R 22 " both_signs ideal model delta sigma weight residual False 2.43 3.16 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 15430 not shown) Planarity restraints: 5422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1712 " 0.038 2.00e-02 2.50e+03 1.76e-02 9.24e+00 pdb=" N9 G A1712 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G A1712 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G A1712 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A1712 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G A1712 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A1712 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G A1712 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A1712 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A1712 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1712 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG P 24 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO P 25 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO P 25 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 25 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 179 " -0.030 2.00e-02 2.50e+03 1.53e-02 6.43e+00 pdb=" N9 A A 179 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A A 179 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A 179 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A A 179 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A A 179 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A A 179 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A A 179 " 0.010 2.00e-02 2.50e+03 pdb=" N3 A A 179 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A A 179 " 0.004 2.00e-02 2.50e+03 ... (remaining 5419 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 26 1.90 - 2.65: 3680 2.65 - 3.40: 86865 3.40 - 4.15: 227081 4.15 - 4.90: 316729 Nonbonded interactions: 634381 Sorted by model distance: nonbonded pdb=" O2 C A2094 " pdb=" N2 G A2474 " model vdw 1.152 2.496 nonbonded pdb=" O2' G A 903 " pdb=" CD2 PHE V 77 " model vdw 1.186 3.340 nonbonded pdb=" O6 G A2428 " pdb=" O6 G A2429 " model vdw 1.330 3.040 nonbonded pdb=" CB ILE Q 88 " pdb=" CD PRO R 51 " model vdw 1.398 3.870 nonbonded pdb=" N2 G A 967 " pdb=" N1 A A2298 " model vdw 1.443 2.600 ... (remaining 634376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 12.410 Check model and map are aligned: 0.800 Set scattering table: 0.480 Process input model: 220.090 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 240.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 78670 Z= 0.385 Angle : 0.879 28.823 119054 Z= 0.475 Chirality : 0.052 1.668 15433 Planarity : 0.004 0.068 5422 Dihedral : 19.207 179.884 37427 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.04 % Favored : 90.08 % Rotamer Outliers : 7.36 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.14), residues: 2047 helix: -4.38 (0.12), residues: 495 sheet: -2.59 (0.25), residues: 347 loop : -2.92 (0.15), residues: 1205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 595 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 128 outliers final: 15 residues processed: 672 average time/residue: 0.8607 time to fit residues: 946.4414 Evaluate side-chains 425 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 410 time to evaluate : 2.740 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6476 time to fit residues: 20.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 192 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 358 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 415 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN D 168 GLN D 173 ASN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 HIS J 54 HIS L 4 HIS L 35 HIS L 83 ASN L 126 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS O 103 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS Q 37 GLN Q 66 ASN ** Q 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN S 37 ASN U 20 GLN U 64 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 78670 Z= 0.348 Angle : 0.792 10.914 119054 Z= 0.395 Chirality : 0.043 0.347 15433 Planarity : 0.006 0.072 5422 Dihedral : 18.778 179.923 33256 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.77 % Favored : 92.04 % Rotamer Outliers : 5.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.16), residues: 2047 helix: -3.29 (0.16), residues: 518 sheet: -2.31 (0.24), residues: 401 loop : -2.47 (0.17), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 428 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 61 residues processed: 484 average time/residue: 0.7578 time to fit residues: 609.5908 Evaluate side-chains 446 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 385 time to evaluate : 2.825 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5782 time to fit residues: 68.0125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 450 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 413 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 134 ASN C 199 GLN D 120 GLN D 168 GLN K 13 ASN L 4 HIS L 35 HIS ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN ** P 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN R 18 GLN S 57 ASN U 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.106 78670 Z= 0.343 Angle : 0.748 14.504 119054 Z= 0.376 Chirality : 0.042 0.340 15433 Planarity : 0.006 0.074 5422 Dihedral : 18.745 178.672 33256 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.55 % Favored : 91.30 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.17), residues: 2047 helix: -2.60 (0.19), residues: 502 sheet: -2.12 (0.25), residues: 393 loop : -2.30 (0.17), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 403 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 42 residues processed: 456 average time/residue: 0.7473 time to fit residues: 566.2683 Evaluate side-chains 406 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 364 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.5585 time to fit residues: 46.2113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 0.9990 chunk 313 optimal weight: 3.9990 chunk 216 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 198 optimal weight: 30.0000 chunk 279 optimal weight: 0.8980 chunk 418 optimal weight: 0.3980 chunk 442 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 396 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN D 168 GLN E 46 GLN E 179 ASN N 61 GLN O 43 GLN P 15 GLN Q 116 GLN R 18 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 78670 Z= 0.154 Angle : 0.598 11.356 119054 Z= 0.302 Chirality : 0.034 0.282 15433 Planarity : 0.005 0.066 5422 Dihedral : 18.270 179.896 33256 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.72 % Favored : 94.14 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2047 helix: -1.97 (0.21), residues: 501 sheet: -1.76 (0.24), residues: 425 loop : -2.09 (0.17), residues: 1121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 422 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 442 average time/residue: 0.7489 time to fit residues: 547.7940 Evaluate side-chains 382 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 364 time to evaluate : 2.775 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5715 time to fit residues: 21.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 6.9990 chunk 251 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 306 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 397 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN D 168 GLN ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN O 43 GLN P 32 HIS ** Q 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.140 78670 Z= 0.456 Angle : 0.837 11.748 119054 Z= 0.415 Chirality : 0.045 0.392 15433 Planarity : 0.006 0.064 5422 Dihedral : 18.683 179.312 33256 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.14 % Favored : 90.72 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.17), residues: 2047 helix: -2.10 (0.20), residues: 505 sheet: -1.89 (0.25), residues: 399 loop : -2.13 (0.17), residues: 1143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 382 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 56 residues processed: 422 average time/residue: 0.7431 time to fit residues: 526.5175 Evaluate side-chains 412 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5351 time to fit residues: 59.5429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 109 optimal weight: 40.0000 chunk 443 optimal weight: 1.9990 chunk 367 optimal weight: 20.0000 chunk 205 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 232 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS D 95 GLN N 27 ASN R 18 GLN S 28 GLN S 67 ASN U 2 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.144 78670 Z= 0.467 Angle : 0.851 14.183 119054 Z= 0.423 Chirality : 0.047 0.409 15433 Planarity : 0.007 0.068 5422 Dihedral : 18.824 178.972 33256 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.87 % Favored : 89.94 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.17), residues: 2047 helix: -2.20 (0.20), residues: 497 sheet: -1.97 (0.24), residues: 410 loop : -2.27 (0.17), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 355 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 389 average time/residue: 0.7448 time to fit residues: 485.8947 Evaluate side-chains 372 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 339 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5273 time to fit residues: 36.3560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 252 optimal weight: 30.0000 chunk 323 optimal weight: 4.9990 chunk 250 optimal weight: 30.0000 chunk 373 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 441 optimal weight: 0.6980 chunk 276 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 83 ASN N 27 ASN Q 116 GLN R 18 GLN S 28 GLN S 67 ASN b 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 78670 Z= 0.308 Angle : 0.709 11.043 119054 Z= 0.357 Chirality : 0.040 0.314 15433 Planarity : 0.005 0.064 5422 Dihedral : 18.502 179.778 33256 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.60 % Favored : 91.26 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.17), residues: 2047 helix: -1.91 (0.21), residues: 505 sheet: -1.88 (0.25), residues: 419 loop : -2.11 (0.18), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 382 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 404 average time/residue: 0.7513 time to fit residues: 506.3375 Evaluate side-chains 382 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 362 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5690 time to fit residues: 23.7056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 300 optimal weight: 0.1980 chunk 218 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 346 optimal weight: 0.8980 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN O 43 GLN P 5 GLN R 18 GLN S 28 GLN S 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 78670 Z= 0.218 Angle : 0.632 11.726 119054 Z= 0.318 Chirality : 0.036 0.284 15433 Planarity : 0.005 0.066 5422 Dihedral : 18.198 179.780 33256 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.18), residues: 2047 helix: -1.62 (0.22), residues: 505 sheet: -1.69 (0.25), residues: 402 loop : -2.00 (0.18), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 376 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 385 average time/residue: 0.8321 time to fit residues: 537.9627 Evaluate side-chains 372 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 362 time to evaluate : 3.148 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6066 time to fit residues: 14.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 2.9990 chunk 422 optimal weight: 4.9990 chunk 385 optimal weight: 8.9990 chunk 411 optimal weight: 2.9990 chunk 247 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 389 optimal weight: 1.9990 chunk 409 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 HIS O 43 GLN R 18 GLN S 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 78670 Z= 0.244 Angle : 0.647 11.375 119054 Z= 0.325 Chirality : 0.037 0.291 15433 Planarity : 0.005 0.062 5422 Dihedral : 18.158 179.214 33256 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.96 % Favored : 91.89 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.18), residues: 2047 helix: -1.51 (0.22), residues: 506 sheet: -1.68 (0.25), residues: 413 loop : -1.97 (0.18), residues: 1128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 369 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 381 average time/residue: 0.7524 time to fit residues: 478.7886 Evaluate side-chains 377 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 360 time to evaluate : 2.781 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.5699 time to fit residues: 20.8454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 302 optimal weight: 0.2980 chunk 456 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 363 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 27 ASN O 43 GLN S 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 78670 Z= 0.271 Angle : 0.673 12.326 119054 Z= 0.338 Chirality : 0.038 0.299 15433 Planarity : 0.005 0.062 5422 Dihedral : 18.167 179.245 33256 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.70 % Favored : 91.16 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 2047 helix: -1.50 (0.22), residues: 502 sheet: -1.60 (0.25), residues: 407 loop : -1.93 (0.18), residues: 1138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 353 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 360 average time/residue: 0.8003 time to fit residues: 483.3831 Evaluate side-chains 360 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 2.854 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6281 time to fit residues: 15.1811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 0.3980 chunk 387 optimal weight: 0.9990 chunk 111 optimal weight: 40.0000 chunk 335 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 373 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 43 GLN S 2 GLN S 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117668 restraints weight = 133547.934| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.01 r_work: 0.3330 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 78670 Z= 0.171 Angle : 0.597 10.687 119054 Z= 0.300 Chirality : 0.034 0.270 15433 Planarity : 0.004 0.062 5422 Dihedral : 17.923 179.768 33256 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.94 % Favored : 92.92 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 2047 helix: -1.28 (0.23), residues: 501 sheet: -1.51 (0.25), residues: 408 loop : -1.84 (0.18), residues: 1138 =============================================================================== Job complete usr+sys time: 11511.74 seconds wall clock time: 206 minutes 18.44 seconds (12378.44 seconds total)