Starting phenix.real_space_refine on Fri Dec 8 17:19:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/12_2023/8c91_16498.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.082 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 2077 5.49 5 S 41 5.16 5 C 28981 2.51 5 N 11042 2.21 5 O 16969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 59110 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1348 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1461 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1121 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain breaks: 1 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 769 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} 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: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 315 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} 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} Chain: "A" Number of atoms: 44635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2077, 44635 Classifications: {'RNA': 2077} Modifications used: {'rna2p_pur': 200, 'rna2p_pyr': 108, 'rna3p_pur': 1021, 'rna3p_pyr': 748} Link IDs: {'rna2p': 308, 'rna3p': 1768} Chain breaks: 5 Time building chain proxies: 23.56, per 1000 atoms: 0.40 Number of scatterers: 59110 At special positions: 0 Unit cell: (170, 203.75, 203.75, 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 41 16.00 P 2077 15.00 O 16969 8.00 N 11042 7.00 C 28981 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: 28.12 Conformation dependent library (CDL) restraints added in 2.7 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 27 sheets defined 31.5% alpha, 18.8% beta 678 base pairs and 1000 stacking pairs defined. Time for finding SS restraints: 22.22 Creating SS restraints... Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.295A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 160 removed outlier: 4.083A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.886A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.687A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.540A 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 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.168A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 131 through 136 removed outlier: 4.374A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 117 removed outlier: 3.957A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.782A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.779A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 89 removed outlier: 4.584A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 11 removed outlier: 3.676A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.585A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 55' Processing helix chain 'P' and resid 96 through 102 removed outlier: 4.011A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG P 102 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.637A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.383A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.078A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.637A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 25 removed outlier: 3.777A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.879A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 62 removed outlier: 4.377A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.543A pdb=" N LEU S 69 " --> pdb=" O ILE S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 10 removed outlier: 3.660A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 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 32 removed outlier: 3.843A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 56 removed outlier: 3.680A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 3.670A pdb=" N ARG 0 12 " --> pdb=" O THR 0 8 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.971A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.898A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 104 removed outlier: 7.011A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 28 removed outlier: 6.866A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.589A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 117 through 118 removed outlier: 4.052A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D 165 " --> pdb=" O GLY D 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.242A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.828A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.602A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.250A pdb=" N TYR J 74 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.517A pdb=" N LEU K 8 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.637A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG P 87 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.518A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.759A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.736A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.946A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP R 95 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.344A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.483A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.849A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.402A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AC6, first strand: chain 'U' and resid 83 through 86 Processing sheet with id=AC7, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC8, first strand: chain '0' and resid 47 through 48 removed outlier: 3.667A pdb=" N TYR 0 48 " --> pdb=" O ARG 0 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 35 through 38 494 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1723 hydrogen bonds 2784 hydrogen bond angles 0 basepair planarities 678 basepair parallelities 1000 stacking parallelities Total time for adding SS restraints: 65.53 Time building geometry restraints manager: 30.11 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: 8654 1.33 - 1.45: 27776 1.45 - 1.57: 23988 1.57 - 1.69: 4148 1.69 - 1.81: 78 Bond restraints: 64644 Sorted by residual: bond pdb=" O5' A A1566 " pdb=" C5' A A1566 " ideal model delta sigma weight residual 1.424 1.453 -0.029 1.50e-02 4.44e+03 3.62e+00 bond pdb=" N GLU T 4 " pdb=" CA GLU T 4 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.41e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N ILE T 2 " pdb=" CA ILE T 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 64639 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.96: 9405 104.96 - 112.21: 37260 112.21 - 119.46: 21348 119.46 - 126.71: 23621 126.71 - 133.97: 5989 Bond angle restraints: 97623 Sorted by residual: angle pdb=" C3' A A1566 " pdb=" C2' A A1566 " pdb=" C1' A A1566 " ideal model delta sigma weight residual 101.50 97.70 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ALA E 161 " pdb=" CA ALA E 161 " pdb=" C ALA E 161 " ideal model delta sigma weight residual 114.62 110.72 3.90 1.14e+00 7.69e-01 1.17e+01 angle pdb=" CA ALA E 161 " pdb=" C ALA E 161 " pdb=" N ARG E 162 " ideal model delta sigma weight residual 119.71 116.36 3.35 1.17e+00 7.31e-01 8.18e+00 angle pdb=" N ARG T 3 " pdb=" CA ARG T 3 " pdb=" C ARG T 3 " ideal model delta sigma weight residual 113.29 107.84 5.45 2.00e+00 2.50e-01 7.43e+00 angle pdb=" O ARG T 3 " pdb=" C ARG T 3 " pdb=" N GLU T 4 " ideal model delta sigma weight residual 121.88 124.75 -2.87 1.07e+00 8.73e-01 7.18e+00 ... (remaining 97618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 35331 34.78 - 69.57: 3843 69.57 - 104.35: 534 104.35 - 139.14: 12 139.14 - 173.92: 6 Dihedral angle restraints: 39726 sinusoidal: 34444 harmonic: 5282 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 41.18 158.82 1 1.50e+01 4.44e-03 8.24e+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 53.21 146.79 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 45.92 -173.92 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 39723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 12403 0.084 - 0.167: 226 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 12631 Sorted by residual: chirality pdb=" P A A1566 " pdb=" OP1 A A1566 " pdb=" OP2 A A1566 " pdb=" O5' A A1566 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ILE T 2 " pdb=" N ILE T 2 " pdb=" C ILE T 2 " pdb=" CB ILE T 2 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 12628 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 32 " -0.003 2.00e-02 2.50e+03 1.45e-02 4.74e+00 pdb=" N1 C A 32 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 32 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 32 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C A 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 32 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C A 32 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1351 " 0.001 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C A1351 " -0.011 2.00e-02 2.50e+03 pdb=" C2 C A1351 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C A1351 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C A1351 " -0.024 2.00e-02 2.50e+03 pdb=" C4 C A1351 " 0.017 2.00e-02 2.50e+03 pdb=" N4 C A1351 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A1351 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A1351 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 175 " 0.018 2.00e-02 2.50e+03 1.07e-02 3.42e+00 pdb=" N9 G A 175 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 175 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 175 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 175 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 175 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G A 175 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 175 " -0.005 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 442 2.50 - 3.10: 40295 3.10 - 3.70: 110989 3.70 - 4.30: 155656 4.30 - 4.90: 213311 Nonbonded interactions: 520693 Sorted by model distance: nonbonded pdb=" O2' C A1462 " pdb=" O2' G A2702 " model vdw 1.896 2.440 nonbonded pdb=" O2' G A 175 " pdb=" O5' A A 176 " model vdw 1.898 2.440 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 1.914 2.440 nonbonded pdb=" O2' G A 636 " pdb=" O2' G A 638 " model vdw 1.925 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.937 2.440 ... (remaining 520688 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.700 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 183.680 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.001 0.034 64644 Z= 0.082 Angle : 0.357 5.830 97623 Z= 0.186 Chirality : 0.025 0.418 12631 Planarity : 0.002 0.029 4596 Dihedral : 21.555 173.924 36312 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % 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: 0.39 (0.20), residues: 1812 helix: 1.76 (0.25), residues: 504 sheet: 0.49 (0.31), residues: 309 loop : -0.59 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 80 HIS 0.002 0.000 HIS E 165 PHE 0.010 0.001 PHE Z 52 TYR 0.005 0.001 TYR Q 44 ARG 0.004 0.000 ARG T 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 363 average time/residue: 0.6248 time to fit residues: 367.5745 Evaluate side-chains 229 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4074 time to fit residues: 3.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 88 ASN L 99 ASN P 40 GLN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN 0 18 HIS 2 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.146 64644 Z= 0.367 Angle : 0.809 15.083 97623 Z= 0.401 Chirality : 0.039 0.240 12631 Planarity : 0.007 0.157 4596 Dihedral : 23.004 173.283 32688 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.84 % Favored : 93.05 % Rotamer: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.06 % 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: -0.92 (0.19), residues: 1812 helix: 0.15 (0.22), residues: 512 sheet: -0.39 (0.28), residues: 358 loop : -1.09 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 15 HIS 0.010 0.002 HIS 0 37 PHE 0.028 0.003 PHE Q 105 TYR 0.018 0.003 TYR C 102 ARG 0.040 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 275 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 278 average time/residue: 0.6099 time to fit residues: 278.9129 Evaluate side-chains 202 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4301 time to fit residues: 4.6666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 292 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 352 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 349 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 282 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: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 64644 Z= 0.275 Angle : 0.604 11.296 97623 Z= 0.306 Chirality : 0.033 0.222 12631 Planarity : 0.005 0.101 4596 Dihedral : 23.060 177.331 32688 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.13 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % 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: -0.98 (0.19), residues: 1812 helix: 0.32 (0.23), residues: 515 sheet: -0.57 (0.27), residues: 377 loop : -1.21 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 15 HIS 0.006 0.002 HIS S 9 PHE 0.016 0.002 PHE Q 105 TYR 0.018 0.002 TYR Q 44 ARG 0.009 0.001 ARG 2 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 265 average time/residue: 0.6021 time to fit residues: 264.9171 Evaluate side-chains 207 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4124 time to fit residues: 3.1071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 353 optimal weight: 10.9990 chunk 374 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 9 ASN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 64644 Z= 0.276 Angle : 0.628 10.778 97623 Z= 0.319 Chirality : 0.034 0.275 12631 Planarity : 0.005 0.123 4596 Dihedral : 23.233 179.318 32688 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.62 % Favored : 92.27 % Rotamer: Outliers : 0.13 % Allowed : 6.20 % Favored : 93.67 % 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: -1.21 (0.19), residues: 1812 helix: 0.21 (0.23), residues: 508 sheet: -0.80 (0.27), residues: 353 loop : -1.36 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 80 HIS 0.007 0.002 HIS 0 37 PHE 0.031 0.002 PHE Z 52 TYR 0.016 0.002 TYR R 83 ARG 0.014 0.001 ARG R 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 267 average time/residue: 0.5889 time to fit residues: 264.6859 Evaluate side-chains 210 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4146 time to fit residues: 3.1227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 5 optimal weight: 40.0000 chunk 278 optimal weight: 30.0000 chunk 154 optimal weight: 0.9980 chunk 319 optimal weight: 10.0000 chunk 258 optimal weight: 40.0000 chunk 0 optimal weight: 30.0000 chunk 191 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 overall best weight: 8.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS 0 4 GLN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 64644 Z= 0.309 Angle : 0.669 11.795 97623 Z= 0.339 Chirality : 0.036 0.263 12631 Planarity : 0.005 0.096 4596 Dihedral : 23.496 178.700 32688 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.40 % Favored : 92.49 % Rotamer: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % 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: -1.41 (0.19), residues: 1812 helix: 0.12 (0.23), residues: 505 sheet: -0.96 (0.27), residues: 379 loop : -1.52 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 15 HIS 0.009 0.002 HIS Y 41 PHE 0.037 0.003 PHE T 51 TYR 0.023 0.002 TYR 0 47 ARG 0.018 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 262 average time/residue: 0.5903 time to fit residues: 260.3301 Evaluate side-chains 204 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.9980 chunk 336 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 219 optimal weight: 50.0000 chunk 92 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 123 optimal weight: 30.0000 chunk 196 optimal weight: 30.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 3 GLN K 9 ASN P 40 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS 0 18 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 64644 Z= 0.210 Angle : 0.570 11.498 97623 Z= 0.289 Chirality : 0.032 0.257 12631 Planarity : 0.004 0.103 4596 Dihedral : 23.349 178.995 32688 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.01 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: -1.23 (0.19), residues: 1812 helix: 0.44 (0.23), residues: 503 sheet: -0.99 (0.26), residues: 393 loop : -1.45 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 15 HIS 0.007 0.001 HIS C 24 PHE 0.030 0.002 PHE Z 52 TYR 0.015 0.002 TYR 0 47 ARG 0.008 0.001 ARG 2 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.5839 time to fit residues: 275.6790 Evaluate side-chains 214 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.307 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 373 optimal weight: 40.0000 chunk 233 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN 0 18 HIS 2 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 64644 Z= 0.369 Angle : 0.734 12.286 97623 Z= 0.369 Chirality : 0.039 0.289 12631 Planarity : 0.006 0.108 4596 Dihedral : 23.723 175.870 32688 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 35.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.66 % Favored : 90.23 % Rotamer: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.77 % 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: -1.78 (0.19), residues: 1812 helix: -0.04 (0.22), residues: 514 sheet: -1.29 (0.27), residues: 347 loop : -1.79 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 15 HIS 0.011 0.002 HIS J 47 PHE 0.032 0.003 PHE Q 105 TYR 0.032 0.003 TYR 0 47 ARG 0.021 0.001 ARG N 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.5883 time to fit residues: 247.0935 Evaluate side-chains 193 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 254 optimal weight: 40.0000 chunk 184 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 5 GLN K 9 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.7193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 64644 Z= 0.283 Angle : 0.645 11.823 97623 Z= 0.326 Chirality : 0.035 0.307 12631 Planarity : 0.005 0.108 4596 Dihedral : 23.684 179.016 32688 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.33 % Favored : 91.56 % Rotamer: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.42 % 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: -1.71 (0.19), residues: 1812 helix: 0.14 (0.23), residues: 497 sheet: -1.31 (0.27), residues: 346 loop : -1.78 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 15 HIS 0.010 0.002 HIS R 89 PHE 0.024 0.002 PHE T 51 TYR 0.025 0.002 TYR 0 47 ARG 0.009 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.5941 time to fit residues: 257.0844 Evaluate side-chains 199 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.8172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 64644 Z= 0.505 Angle : 0.899 14.843 97623 Z= 0.448 Chirality : 0.046 0.369 12631 Planarity : 0.007 0.106 4596 Dihedral : 24.296 172.961 32688 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 46.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.31 % Favored : 88.58 % Rotamer: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.47 (0.18), residues: 1812 helix: -0.72 (0.21), residues: 517 sheet: -1.69 (0.26), residues: 339 loop : -2.16 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP T 80 HIS 0.021 0.003 HIS J 47 PHE 0.031 0.003 PHE T 51 TYR 0.041 0.003 TYR 0 47 ARG 0.013 0.001 ARG L 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.5906 time to fit residues: 235.5386 Evaluate side-chains 183 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 31 optimal weight: 0.0050 chunk 237 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 overall best weight: 7.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 64644 Z= 0.273 Angle : 0.665 11.799 97623 Z= 0.336 Chirality : 0.036 0.351 12631 Planarity : 0.005 0.084 4596 Dihedral : 23.974 178.975 32688 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 30.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.61 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.18), residues: 1812 helix: -0.09 (0.23), residues: 496 sheet: -1.58 (0.26), residues: 343 loop : -1.96 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 125 HIS 0.014 0.002 HIS J 47 PHE 0.021 0.002 PHE K 112 TYR 0.025 0.002 TYR 0 47 ARG 0.011 0.001 ARG R 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.6307 time to fit residues: 264.6219 Evaluate side-chains 195 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 30.0000 chunk 327 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 315 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 5 GLN K 9 ASN N 107 ASN Q 80 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044459 restraints weight = 541287.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.045547 restraints weight = 232020.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.046180 restraints weight = 150123.528| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 64644 Z= 0.144 Angle : 0.546 12.418 97623 Z= 0.273 Chirality : 0.031 0.282 12631 Planarity : 0.004 0.053 4596 Dihedral : 23.481 176.988 32688 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % 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: -1.48 (0.19), residues: 1812 helix: 0.45 (0.23), residues: 492 sheet: -1.21 (0.27), residues: 337 loop : -1.68 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 15 HIS 0.011 0.001 HIS J 47 PHE 0.021 0.002 PHE N 102 TYR 0.014 0.002 TYR C 102 ARG 0.010 0.001 ARG R 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6670.31 seconds wall clock time: 123 minutes 24.45 seconds (7404.45 seconds total)