Starting phenix.real_space_refine (version: 1.19rc7) on Fri Jan 8 01:46:02 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc7_4382/01_2021/6gc7_4382.pdb" } resolution = 4.3 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= 0.070 sd= 0.500 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 54410 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 40850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1901, 40850 Classifications: {'RNA': 1901} Modifications used: {'rna3p_pyr': 684, 'rna2p_pur': 182, 'rna3p_pur': 933, 'rna2p_pyr': 102} Link IDs: {'rna3p': 1616, 'rna2p': 284} Chain breaks: 8 Chain: "D" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1366 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 28.93, per 1000 atoms: 0.53 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 54410 At special positions: 0 Unit cell: (210.8, 163.68, 210.8, 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 39 16.00 P 1901 15.00 O 15576 8.00 N 10181 7.00 C 26713 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 Amimo 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: 24.66 Conformation dependent library (CDL) restraints added in 2.9 seconds 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 30.0% alpha, 19.9% beta 525 base pairs and 981 stacking pairs defined. Time for finding SS restraints: 22.09 Creating SS restraints... Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.645A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.844A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.574A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.078A pdb=" N ILE E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.778A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.719A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.671A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.094A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.557A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.175A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.929A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.801A pdb=" N SER K 117 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.883A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 3.748A 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 29 through 33 removed outlier: 3.623A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 33' Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.215A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'L' and resid 136 through 139 removed outlier: 3.724A pdb=" N GLY L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 136 through 139' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.641A pdb=" N ARG N 17 " --> pdb=" O ASN N 13 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 55 removed outlier: 3.508A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 61 through 69 removed outlier: 3.650A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 78 removed outlier: 3.668A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.562A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.544A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.707A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 4.207A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.979A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 69 removed outlier: 3.981A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.657A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.686A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.744A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.735A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 removed outlier: 3.891A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 9 removed outlier: 4.137A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.691A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.575A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 30 removed outlier: 3.528A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 44 removed outlier: 4.328A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.176A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 16 removed outlier: 3.572A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 26 through 38 Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.856A pdb=" N THR Z 22 " --> pdb=" O LYS Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 48 Processing sheet with id=AA1, first strand: chain 'D' and resid 21 through 28 removed outlier: 6.664A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.235A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.992A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 170 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 122 through 124 removed outlier: 3.589A pdb=" N LEU J 57 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 73 through 76 Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 10 removed outlier: 4.068A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ARG K 17 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA K 46 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL K 19 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS K 44 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N CYS K 21 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR K 42 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.719A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL P 60 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.719A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG P 71 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL P 60 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 121 through 122 Processing sheet with id=AB2, first strand: chain 'N' and resid 33 through 36 removed outlier: 3.548A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.842A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.219A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.680A pdb=" N PHE S 75 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 82 through 87 removed outlier: 3.601A pdb=" N ARG S 84 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP S 94 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.744A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'U' and resid 63 through 65 removed outlier: 3.519A pdb=" N ILE U 11 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA U 70 " --> pdb=" O ILE U 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.565A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 83 through 86 removed outlier: 3.624A pdb=" N GLY U 83 " --> pdb=" O PHE U 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC6, first strand: chain 'Z' and resid 34 through 37 removed outlier: 3.956A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. NA hbond rejected: pdb=" O2 C A1727 " pdb=" N2 G A1734 " distance=3.92 NA hbond rejected: pdb=" O2 C A1728 " pdb=" N2 G A1733 " distance=3.59 NA hbond rejected: pdb=" O2 C A1172 " pdb=" N2 G A1177 " distance=4.00 NA hbond rejected: pdb=" N4 C A1278 " pdb=" O6 G A1292 " distance=3.67 NA hbond rejected: pdb=" O2 C A 998 " pdb=" N2 G A1157 " distance=3.66 NA hbond rejected: pdb=" N4 C A 398 " pdb=" O6 G A 376 " distance=3.82 NA hbond rejected: pdb=" O2 C A1605 " pdb=" N2 G A1309 " distance=3.88 NA hbond rejected: pdb=" N4 C A1686 " pdb=" O6 G A1702 " distance=3.60 NA hbond rejected: pdb=" N4 C A 671 " pdb=" O6 G A 809 " distance=3.87 NA hbond rejected: pdb=" N4 C A2730 " pdb=" O6 G A2677 " distance=3.43 NA hbond rejected: pdb=" O2 C A 937 " pdb=" N2 G A 841 " distance=3.41 NA hbond rejected: pdb=" O2 C A1686 " pdb=" N2 G A1703 " distance=3.48 NA hbond rejected: pdb=" O2 C A1541 " pdb=" N2 G A1530 " distance=3.57 NA hbond rejected: pdb=" N4 C A 209 " pdb=" O6 G A 187 " distance=3.77 Restraints generated for nucleic acids: 1324 hydrogen bonds 2100 hydrogen bond angles 0 basepair planarities 525 basepair parallelities 981 stacking parallelities Total time for adding SS restraints: 66.60 Time building geometry restraints manager: 26.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7772 1.33 - 1.45: 25398 1.45 - 1.57: 22433 1.57 - 1.69: 3795 1.69 - 1.81: 75 Bond restraints: 59473 Sorted by residual: bond pdb=" CA ASN U 98 " pdb=" CB ASN U 98 " ideal model delta sigma weight residual 1.532 1.571 -0.040 1.33e-02 5.65e+03 8.87e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.573 -0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.10e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.61e+00 bond pdb=" C ALA K 119 " pdb=" N PRO K 120 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.19e-02 7.06e+03 3.36e+00 ... (remaining 59468 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.62: 11512 106.62 - 113.47: 35418 113.47 - 120.31: 21850 120.31 - 127.15: 16302 127.15 - 134.00: 4660 Bond angle restraints: 89742 Sorted by residual: angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.66 -11.96 1.80e+00 3.09e-01 4.41e+01 angle pdb=" C GLN Y 45 " pdb=" N VAL Y 46 " pdb=" CA VAL Y 46 " ideal model delta sigma weight residual 121.97 132.94 -10.97 1.80e+00 3.09e-01 3.71e+01 angle pdb=" C VAL 0 53 " pdb=" N ILE 0 54 " pdb=" CA ILE 0 54 " ideal model delta sigma weight residual 120.77 127.94 -7.17 1.31e+00 5.83e-01 2.99e+01 angle pdb=" C GLY L 114 " pdb=" N GLU L 115 " pdb=" CA GLU L 115 " ideal model delta sigma weight residual 122.46 129.91 -7.45 1.41e+00 5.03e-01 2.79e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 124.82 133.74 -8.92 1.78e+00 3.16e-01 2.51e+01 ... (remaining 89737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 30307 35.16 - 70.32: 916 70.32 - 105.48: 73 105.48 - 140.64: 2 140.64 - 175.80: 7 Dihedral angle restraints: 31305 sinusoidal: 26367 harmonic: 4938 Sorted by residual: dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 43.94 156.06 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' U A 646 " pdb=" C1' U A 646 " pdb=" N1 U A 646 " pdb=" C2 U A 646 " ideal model delta sinusoidal sigma weight residual 200.00 44.19 155.81 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 64.26 135.74 1 1.50e+01 4.44e-03 7.32e+01 ... (remaining 31302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 11102 0.070 - 0.141: 454 0.141 - 0.211: 41 0.211 - 0.281: 3 0.281 - 0.352: 3 Chirality restraints: 11603 Sorted by residual: chirality pdb=" CB VAL L 110 " pdb=" CA VAL L 110 " pdb=" CG1 VAL L 110 " pdb=" CG2 VAL L 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 11600 not shown) Planarity restraints: 4258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 635 " 0.006 2.00e-02 2.50e+03 1.75e-02 6.90e+00 pdb=" N1 C A 635 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C A 635 " 0.040 2.00e-02 2.50e+03 pdb=" O2 C A 635 " -0.031 2.00e-02 2.50e+03 pdb=" N3 C A 635 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A 635 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C A 635 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C A 635 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 635 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR Z 40 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO Z 41 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO Z 41 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO Z 41 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.028 2.00e-02 2.50e+03 1.64e-02 6.02e+00 pdb=" N1 U A1736 " 0.037 2.00e-02 2.50e+03 pdb=" C2 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.000 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.006 2.00e-02 2.50e+03 ... (remaining 4255 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 10727 2.78 - 3.31: 43025 3.31 - 3.84: 113797 3.84 - 4.37: 130828 4.37 - 4.90: 174227 Nonbonded interactions: 472604 Sorted by model distance: nonbonded pdb=" O2 C A 269 " pdb=" N2 G A 370 " model vdw 2.251 2.496 nonbonded pdb=" O2 C A 335 " pdb=" OG SER U 67 " model vdw 2.261 2.440 nonbonded pdb=" O2' U A 571 " pdb=" OP2 U A 573 " model vdw 2.268 2.440 nonbonded pdb=" O ILE S 35 " pdb=" OG1 THR S 39 " model vdw 2.281 2.440 nonbonded pdb=" O2' C A 239 " pdb=" O2' G A 622 " model vdw 2.284 2.440 ... (remaining 472599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 54410 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1901 5.49 5 S 39 5.16 5 C 26713 2.51 5 N 10181 2.21 5 O 15576 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 1.190 Set model interpretation parameters: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.920 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.270 Process input model: 199.240 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.210 Internal consistency checks: 0.000 Total: 213.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.057 59473 Angle : 0.671 12.122 89742 Chirality : 0.031 0.352 11603 Planarity : 0.004 0.063 4258 Dihedral : 13.130 175.805 28113 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.93 % Favored : 93.95 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 1702 helix: -4.15 (0.12), residues: 445 sheet: -1.63 (0.28), residues: 303 loop : -2.61 (0.15), residues: 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 788 time to evaluate : 3.396 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 789 average time/residue: 0.8384 time to fit residues: 666.3417 Evaluate side-chains 415 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 414 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4993 time to fit residues: 3.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 173 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 9 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN R 6 GLN R 86 GLN S 7 HIS U 44 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.096 59473 Angle : 0.771 9.513 89742 Chirality : 0.041 0.265 11603 Planarity : 0.006 0.092 4258 Dihedral : 15.393 176.531 24710 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 30.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.89 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.18), residues: 1702 helix: -1.63 (0.21), residues: 472 sheet: -1.22 (0.28), residues: 317 loop : -2.04 (0.18), residues: 913 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 5 poor density : 533 time to evaluate : 3.407 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 535 average time/residue: 0.8028 time to fit residues: 434.4021 Evaluate side-chains 386 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 385 time to evaluate : 3.002 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6134 time to fit residues: 3.5925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 325 optimal weight: 6.9990 chunk 351 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN K 3 GLN K 9 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 11 GLN P 65 ASN P 76 HIS Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN Y 15 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.054 59473 Angle : 0.525 12.620 89742 Chirality : 0.030 0.226 11603 Planarity : 0.005 0.084 4258 Dihedral : 14.492 179.538 24710 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.01 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.99 (0.19), residues: 1702 helix: -0.70 (0.23), residues: 480 sheet: -0.86 (0.30), residues: 292 loop : -1.84 (0.18), residues: 930 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 540 time to evaluate : 3.009 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 540 average time/residue: 0.7586 time to fit residues: 414.1292 Evaluate side-chains 391 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 391 time to evaluate : 3.092 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 326 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 309 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 6.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.060 59473 Angle : 0.655 11.883 89742 Chirality : 0.037 0.232 11603 Planarity : 0.005 0.074 4258 Dihedral : 15.291 172.016 24710 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 27.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.05 % Favored : 91.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.03 (0.19), residues: 1702 helix: -0.69 (0.23), residues: 486 sheet: -1.07 (0.28), residues: 311 loop : -1.83 (0.19), residues: 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 477 time to evaluate : 3.402 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.7566 time to fit residues: 365.7483 Evaluate side-chains 366 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 366 time to evaluate : 3.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 0.0030 chunk 142 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 310 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 overall best weight: 3.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.038 59473 Angle : 0.525 10.310 89742 Chirality : 0.030 0.242 11603 Planarity : 0.004 0.092 4258 Dihedral : 14.745 175.270 24710 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.72 (0.19), residues: 1702 helix: -0.31 (0.24), residues: 486 sheet: -0.97 (0.29), residues: 299 loop : -1.67 (0.19), residues: 917 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 466 time to evaluate : 3.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.7229 time to fit residues: 341.6103 Evaluate side-chains 373 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 373 time to evaluate : 3.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 160 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN Z 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.071 59473 Angle : 0.704 11.454 89742 Chirality : 0.039 0.323 11603 Planarity : 0.005 0.063 4258 Dihedral : 15.676 172.681 24710 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.14 (0.19), residues: 1702 helix: -0.78 (0.22), residues: 494 sheet: -1.26 (0.27), residues: 337 loop : -1.86 (0.19), residues: 871 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 452 time to evaluate : 3.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.7348 time to fit residues: 336.8335 Evaluate side-chains 352 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 352 time to evaluate : 3.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 0.9990 chunk 39 optimal weight: 40.0000 chunk 197 optimal weight: 5.9990 chunk 252 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 210 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 ASN K 3 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 86 GLN S 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.040 59473 Angle : 0.514 10.941 89742 Chirality : 0.029 0.270 11603 Planarity : 0.004 0.038 4258 Dihedral : 14.756 174.888 24710 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.34 % Favored : 92.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.55 (0.19), residues: 1702 helix: -0.19 (0.24), residues: 483 sheet: -0.75 (0.31), residues: 260 loop : -1.57 (0.19), residues: 959 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 480 time to evaluate : 3.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.7297 time to fit residues: 354.9933 Evaluate side-chains 385 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 385 time to evaluate : 3.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 206 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 ASN K 3 GLN ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 86 GLN ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN U 45 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.046 59473 Angle : 0.570 10.158 89742 Chirality : 0.032 0.266 11603 Planarity : 0.004 0.051 4258 Dihedral : 15.050 173.700 24710 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.28 % Favored : 91.66 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.67 (0.19), residues: 1702 helix: -0.30 (0.24), residues: 485 sheet: -1.01 (0.29), residues: 290 loop : -1.59 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 447 time to evaluate : 3.020 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 449 average time/residue: 0.6974 time to fit residues: 317.5794 Evaluate side-chains 364 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 363 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5804 time to fit residues: 3.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 252 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 ASN K 3 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 87 GLN S 31 GLN Z 33 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.041 59473 Angle : 0.508 10.783 89742 Chirality : 0.029 0.239 11603 Planarity : 0.004 0.054 4258 Dihedral : 14.636 177.391 24710 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.42 (0.20), residues: 1702 helix: -0.04 (0.24), residues: 486 sheet: -0.72 (0.31), residues: 259 loop : -1.50 (0.19), residues: 957 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 458 time to evaluate : 3.031 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 0.7132 time to fit residues: 331.1806 Evaluate side-chains 375 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 9.9990 chunk 340 optimal weight: 0.9980 chunk 207 optimal weight: 0.0030 chunk 161 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 328 optimal weight: 0.6980 chunk 284 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 174 optimal weight: 50.0000 overall best weight: 3.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN K 5 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 HIS R 86 GLN R 87 GLN S 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.8641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.048 59473 Angle : 0.546 15.902 89742 Chirality : 0.030 0.260 11603 Planarity : 0.004 0.048 4258 Dihedral : 14.852 174.441 24710 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.70 % Favored : 92.24 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.63 (0.19), residues: 1702 helix: -0.29 (0.23), residues: 501 sheet: -1.03 (0.30), residues: 271 loop : -1.54 (0.19), residues: 930 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield and 0 Emsley and 1702 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 440 time to evaluate : 3.105 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 441 average time/residue: 0.7278 time to fit residues: 325.9709 Evaluate side-chains 353 residues out of total 1418 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 353 time to evaluate : 3.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.3980 chunk 302 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 41 optimal weight: 30.0000 chunk 78 optimal weight: 40.0000 chunk 284 optimal weight: 0.0870 chunk 119 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 overall best weight: 2.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 86 GLN R 87 GLN S 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.083972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.059924 restraints weight = 301772.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061875 restraints weight = 118105.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.063003 restraints weight = 71897.453| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.036 59473 ANGLE : 0.523 13.650 89742 CHIRALITY : 0.029 0.234 11603 PLANARITY : 0.004 0.040 4258 DIHEDRAL : 14.715 176.395 24710 MIN NONBONDED DISTANCE : 1.982 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 18.98 RAMACHANDRAN PLOT: OUTLIERS : 0.06 % ALLOWED : 7.81 % FAVORED : 92.13 % ROTAMER OUTLIERS : 0.14 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.06 % 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: -1.43 (0.19), RESIDUES: 1702 HELIX: -0.12 (0.24), RESIDUES: 487 SHEET: -0.64 (0.31), RESIDUES: 260 LOOP : -1.50 (0.19), RESIDUES: 955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.8676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.036 59473 Angle : 0.523 13.650 89742 Chirality : 0.029 0.234 11603 Planarity : 0.004 0.040 4258 Dihedral : 14.715 176.395 24710 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.81 % Favored : 92.13 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.43 (0.19), residues: 1702 helix: -0.12 (0.24), residues: 487 sheet: -0.64 (0.31), residues: 260 loop : -1.50 (0.19), residues: 955 =============================================================================== Job complete usr+sys time: 8489.40 seconds wall clock time: 159 minutes 41.57 seconds (9581.57 seconds total)