Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 11:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/08_2023/8c92_16499.pdb" } resolution = 3.79 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= 0.076 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 1873 5.49 5 S 37 5.16 5 C 26245 2.51 5 N 9999 2.21 5 O 15335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 53489 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 40250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 40250 Classifications: {'RNA': 1873} Modifications used: {'rna2p_pur': 171, 'rna2p_pyr': 98, 'rna3p_pur': 927, 'rna3p_pyr': 677} Link IDs: {'rna2p': 269, 'rna3p': 1603} Chain breaks: 6 Chain: "D" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1306 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "E" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1438 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} 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: 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: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} 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: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 312 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 19.67, per 1000 atoms: 0.37 Number of scatterers: 53489 At special positions: 0 Unit cell: (151.25, 205, 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 37 16.00 P 1873 15.00 O 15335 8.00 N 9999 7.00 C 26245 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: 22.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 22 sheets defined 34.4% alpha, 18.1% beta 618 base pairs and 876 stacking pairs defined. Time for finding SS restraints: 18.28 Creating SS restraints... Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.837A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 4.098A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.596A pdb=" N ILE E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.251A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 4.021A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.044A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.729A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.927A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 33 removed outlier: 3.902A pdb=" N GLY L 31 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 33' Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.534A pdb=" N ILE L 73 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.623A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.741A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.985A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.550A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.732A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.094A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.900A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.256A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 23 removed outlier: 4.029A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.693A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.225A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 8 Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.103A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Y' and resid 2 through 8 removed outlier: 4.085A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 33 removed outlier: 3.728A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.265A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.049A 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 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.950A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.747A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.894A 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 'D' and resid 169 through 175 removed outlier: 5.124A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.422A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 48 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 82 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.115A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 120 removed outlier: 7.075A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.163A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 3.745A 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 75 Processing sheet with id=AA7, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.597A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE K 41 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 6.960A 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: 3.893A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.486A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.101A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.714A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.330A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 72 through 77 Processing sheet with id=AB5, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.846A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB7, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.958A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR T 86 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 33 through 35 removed outlier: 7.027A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.985A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AC2, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC4, first strand: chain 'Z' and resid 35 through 37 removed outlier: 3.885A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1571 hydrogen bonds 2526 hydrogen bond angles 0 basepair planarities 618 basepair parallelities 876 stacking parallelities Total time for adding SS restraints: 47.16 Time building geometry restraints manager: 24.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9943 1.34 - 1.46: 24957 1.46 - 1.58: 19762 1.58 - 1.70: 3739 1.70 - 1.82: 71 Bond restraints: 58472 Sorted by residual: bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.572 -0.092 1.50e-02 4.44e+03 3.75e+01 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N ALA 0 1 " pdb=" CA ALA 0 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 58467 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.23: 11374 107.23 - 113.91: 36765 113.91 - 120.59: 21023 120.59 - 127.26: 14958 127.26 - 133.94: 4141 Bond angle restraints: 88261 Sorted by residual: angle pdb=" N ALA T 13 " pdb=" CA ALA T 13 " pdb=" C ALA T 13 " ideal model delta sigma weight residual 108.13 112.39 -4.26 9.00e-01 1.23e+00 2.24e+01 angle pdb=" N VAL K 63 " pdb=" CA VAL K 63 " pdb=" C VAL K 63 " ideal model delta sigma weight residual 111.81 108.98 2.83 8.60e-01 1.35e+00 1.08e+01 angle pdb=" N LEU Y 57 " pdb=" CA LEU Y 57 " pdb=" CB LEU Y 57 " ideal model delta sigma weight residual 114.17 110.71 3.46 1.14e+00 7.69e-01 9.20e+00 angle pdb=" CB MET R 1 " pdb=" CG MET R 1 " pdb=" SD MET R 1 " ideal model delta sigma weight residual 112.70 120.63 -7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" CG MET N 110 " pdb=" SD MET N 110 " pdb=" CE MET N 110 " ideal model delta sigma weight residual 100.90 106.23 -5.33 2.20e+00 2.07e-01 5.87e+00 ... (remaining 88256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 29865 35.87 - 71.73: 805 71.73 - 107.60: 71 107.60 - 143.46: 17 143.46 - 179.33: 5 Dihedral angle restraints: 30763 sinusoidal: 25931 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual 232.00 52.67 179.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 828 " pdb=" C1' U A 828 " pdb=" N1 U A 828 " pdb=" C2 U A 828 " ideal model delta sinusoidal sigma weight residual -128.00 44.49 -172.49 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 10.78 -138.78 1 1.70e+01 3.46e-03 5.82e+01 ... (remaining 30760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 8578 0.029 - 0.057: 2471 0.057 - 0.086: 180 0.086 - 0.114: 153 0.114 - 0.143: 45 Chirality restraints: 11427 Sorted by residual: chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1' G A1343 " pdb=" O4' G A1343 " pdb=" C2' G A1343 " pdb=" N9 G A1343 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" C3' A A1420 " pdb=" C4' A A1420 " pdb=" O3' A A1420 " pdb=" C2' A A1420 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 11424 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " 0.004 2.00e-02 2.50e+03 1.53e-02 5.28e+00 pdb=" N1 C A 269 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.025 2.00e-02 2.50e+03 pdb=" N3 C A 269 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 468 " 0.017 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" N9 G A 468 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G A 468 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 468 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 468 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 468 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G A 468 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G A 468 " 0.020 2.00e-02 2.50e+03 pdb=" C2 G A 468 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G A 468 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 468 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 468 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1333 " 0.006 2.00e-02 2.50e+03 1.30e-02 5.07e+00 pdb=" N9 G A1333 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G A1333 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A1333 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A1333 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A1333 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G A1333 " -0.034 2.00e-02 2.50e+03 pdb=" N2 G A1333 " 0.021 2.00e-02 2.50e+03 pdb=" N3 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A1333 " 0.002 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 326 2.48 - 3.08: 34967 3.08 - 3.69: 102271 3.69 - 4.29: 141937 4.29 - 4.90: 195261 Nonbonded interactions: 474762 Sorted by model distance: nonbonded pdb=" O2' G A 214 " pdb=" O4' G A 215 " model vdw 1.872 2.440 nonbonded pdb=" OP2 G A1521 " pdb=" O2' A A1522 " model vdw 1.916 2.440 nonbonded pdb=" OP2 G A 989 " pdb=" OG SER Z 11 " model vdw 1.942 2.440 nonbonded pdb=" O2' G A1666 " pdb=" O4' G A1667 " model vdw 1.966 2.440 nonbonded pdb=" O3' C A2730 " pdb=" OG SER D 174 " model vdw 1.973 2.440 ... (remaining 474757 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.900 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 144.310 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.002 0.092 58472 Z= 0.096 Angle : 0.377 7.931 88261 Z= 0.197 Chirality : 0.026 0.143 11427 Planarity : 0.002 0.034 4167 Dihedral : 13.238 179.329 27637 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer Outliers : 0.00 % 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: 0.46 (0.21), residues: 1660 helix: 1.69 (0.25), residues: 515 sheet: 0.50 (0.32), residues: 248 loop : -0.58 (0.21), residues: 897 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.5182 time to fit residues: 273.9794 Evaluate side-chains 208 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 204 optimal weight: 0.2980 chunk 317 optimal weight: 0.8980 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 GLN K 5 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN 0 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 58472 Z= 0.244 Angle : 0.549 9.484 88261 Z= 0.275 Chirality : 0.030 0.185 11427 Planarity : 0.004 0.041 4167 Dihedral : 13.673 179.435 24328 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer Outliers : 2.52 % 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: -0.09 (0.21), residues: 1660 helix: 0.85 (0.24), residues: 512 sheet: 0.19 (0.30), residues: 276 loop : -0.66 (0.21), residues: 872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 250 average time/residue: 0.5267 time to fit residues: 223.1973 Evaluate side-chains 221 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3736 time to fit residues: 20.1023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 318 optimal weight: 6.9990 chunk 343 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 315 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Z 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 58472 Z= 0.286 Angle : 0.581 9.368 88261 Z= 0.295 Chirality : 0.032 0.190 11427 Planarity : 0.005 0.044 4167 Dihedral : 14.135 178.461 24328 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.43 % Rotamer Outliers : 2.09 % 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: -0.62 (0.20), residues: 1660 helix: 0.29 (0.23), residues: 514 sheet: -0.10 (0.30), residues: 286 loop : -0.91 (0.21), residues: 860 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 219 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 237 average time/residue: 0.5281 time to fit residues: 215.0625 Evaluate side-chains 212 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3981 time to fit residues: 15.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 8.9990 chunk 239 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 213 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 58472 Z= 0.368 Angle : 0.698 12.373 88261 Z= 0.352 Chirality : 0.037 0.225 11427 Planarity : 0.006 0.074 4167 Dihedral : 15.006 176.588 24328 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.11 % Rotamer Outliers : 3.89 % 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: -1.17 (0.20), residues: 1660 helix: -0.19 (0.22), residues: 506 sheet: -0.68 (0.30), residues: 292 loop : -1.12 (0.21), residues: 862 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 36 residues processed: 240 average time/residue: 0.5344 time to fit residues: 217.6573 Evaluate side-chains 227 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3941 time to fit residues: 29.0939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 233 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 303 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 58472 Z= 0.172 Angle : 0.518 9.945 88261 Z= 0.264 Chirality : 0.030 0.239 11427 Planarity : 0.004 0.046 4167 Dihedral : 14.499 176.620 24328 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 1.44 % 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: -0.83 (0.20), residues: 1660 helix: 0.16 (0.23), residues: 512 sheet: -0.29 (0.31), residues: 268 loop : -1.02 (0.21), residues: 880 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 2.055 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 240 average time/residue: 0.5346 time to fit residues: 221.3853 Evaluate side-chains 212 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4329 time to fit residues: 8.6219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 338 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 58472 Z= 0.419 Angle : 0.712 11.714 88261 Z= 0.357 Chirality : 0.038 0.235 11427 Planarity : 0.005 0.075 4167 Dihedral : 15.126 176.649 24328 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.81 % 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: -1.30 (0.20), residues: 1660 helix: -0.22 (0.22), residues: 512 sheet: -0.67 (0.30), residues: 283 loop : -1.29 (0.21), residues: 865 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 213 average time/residue: 0.5190 time to fit residues: 189.6110 Evaluate side-chains 208 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3884 time to fit residues: 20.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.0980 chunk 38 optimal weight: 40.0000 chunk 192 optimal weight: 0.5980 chunk 247 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 337 optimal weight: 7.9990 chunk 211 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 155 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 58472 Z= 0.127 Angle : 0.510 12.807 88261 Z= 0.257 Chirality : 0.029 0.248 11427 Planarity : 0.004 0.044 4167 Dihedral : 14.496 176.274 24328 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.65 % 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: -0.88 (0.20), residues: 1660 helix: 0.22 (0.23), residues: 512 sheet: -0.39 (0.31), residues: 274 loop : -1.12 (0.21), residues: 874 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 236 time to evaluate : 2.036 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 240 average time/residue: 0.5200 time to fit residues: 213.6162 Evaluate side-chains 212 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3840 time to fit residues: 5.7566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 9.9990 chunk 134 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 0.1980 chunk 229 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 overall best weight: 7.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 58472 Z= 0.340 Angle : 0.640 10.213 88261 Z= 0.322 Chirality : 0.035 0.273 11427 Planarity : 0.005 0.047 4167 Dihedral : 14.928 176.963 24328 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1660 helix: -0.14 (0.23), residues: 514 sheet: -0.60 (0.30), residues: 277 loop : -1.30 (0.21), residues: 869 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 211 average time/residue: 0.5292 time to fit residues: 190.1089 Evaluate side-chains 209 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3943 time to fit residues: 14.8537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 313 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 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 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 58472 Z= 0.266 Angle : 0.587 12.200 88261 Z= 0.297 Chirality : 0.033 0.273 11427 Planarity : 0.004 0.063 4167 Dihedral : 14.893 177.221 24328 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer Outliers : 0.72 % 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: -1.28 (0.20), residues: 1660 helix: -0.11 (0.23), residues: 512 sheet: -0.66 (0.31), residues: 273 loop : -1.34 (0.21), residues: 875 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 207 average time/residue: 0.5371 time to fit residues: 191.1103 Evaluate side-chains 200 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4152 time to fit residues: 5.9519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 8.9990 chunk 332 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 348 optimal weight: 0.2980 chunk 320 optimal weight: 0.5980 chunk 277 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 170 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 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 57 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 58472 Z= 0.148 Angle : 0.510 13.579 88261 Z= 0.257 Chirality : 0.029 0.280 11427 Planarity : 0.004 0.046 4167 Dihedral : 14.551 176.796 24328 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 0.65 % 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: -0.97 (0.20), residues: 1660 helix: 0.21 (0.23), residues: 504 sheet: -0.57 (0.31), residues: 279 loop : -1.15 (0.21), residues: 877 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 220 average time/residue: 0.5300 time to fit residues: 201.4584 Evaluate side-chains 211 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3877 time to fit residues: 5.8160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 0.0270 chunk 295 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 256 optimal weight: 0.0870 chunk 40 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 278 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 4.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.052760 restraints weight = 304967.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054033 restraints weight = 125297.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054809 restraints weight = 83193.059| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 58472 Z= 0.231 Angle : 0.546 13.577 88261 Z= 0.276 Chirality : 0.031 0.282 11427 Planarity : 0.004 0.044 4167 Dihedral : 14.598 177.458 24328 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.29 % 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: -1.08 (0.20), residues: 1660 helix: 0.12 (0.23), residues: 508 sheet: -0.64 (0.31), residues: 278 loop : -1.22 (0.21), residues: 874 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5614.42 seconds wall clock time: 104 minutes 6.25 seconds (6246.25 seconds total)