Starting phenix.real_space_refine on Tue Sep 24 18:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/09_2024/8c92_16499.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/09_2024/8c92_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_16499/09_2024/8c92_16499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/09_2024/8c92_16499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/09_2024/8c92_16499.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/09_2024/8c92_16499.cif" } 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. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 21.90, per 1000 atoms: 0.41 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.08 Conformation dependent library (CDL) restraints added in 1.9 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: 19.65 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: 47.42 Time building geometry restraints manager: 11.16 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: 0.00 - 1.59: 87668 1.59 - 3.17: 522 3.17 - 4.76: 64 4.76 - 6.35: 4 6.35 - 7.93: 3 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: 32888 35.87 - 71.73: 4030 71.73 - 107.60: 487 107.60 - 143.46: 17 143.46 - 179.33: 5 Dihedral angle restraints: 37427 sinusoidal: 32595 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 37424 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 3.040 nonbonded pdb=" OP2 G A1521 " pdb=" O2' A A1522 " model vdw 1.916 3.040 nonbonded pdb=" OP2 G A 989 " pdb=" OG SER Z 11 " model vdw 1.942 3.040 nonbonded pdb=" O2' G A1666 " pdb=" O4' G A1667 " model vdw 1.966 3.040 nonbonded pdb=" O3' C A2730 " pdb=" OG SER D 174 " model vdw 1.973 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.630 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 124.220 Find NCS groups from input model: 0.390 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: 130.310 ------------------------------------------------------------------------------- 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 : 22.722 179.329 34301 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 % Allowed : 0.14 % Favored : 99.86 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 30 HIS 0.006 0.001 HIS R 82 PHE 0.006 0.001 PHE S 75 TYR 0.011 0.001 TYR N 112 ARG 0.004 0.000 ARG Z 44 *********************** 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 : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLN cc_start: 0.8247 (mt0) cc_final: 0.7959 (mm110) REVERT: J 53 TYR cc_start: 0.7762 (m-80) cc_final: 0.7514 (m-80) REVERT: J 138 GLN cc_start: 0.7246 (mp10) cc_final: 0.6871 (mp10) REVERT: K 41 ILE cc_start: 0.8491 (pt) cc_final: 0.8274 (tt) REVERT: K 75 SER cc_start: 0.8237 (m) cc_final: 0.7666 (p) REVERT: L 126 ARG cc_start: 0.1247 (mtm180) cc_final: 0.0636 (ttp80) REVERT: N 35 LYS cc_start: 0.8806 (tttm) cc_final: 0.8363 (ttpp) REVERT: S 12 SER cc_start: 0.9087 (p) cc_final: 0.8879 (p) REVERT: S 110 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7828 (tpp-160) REVERT: 0 11 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8505 (mtmm) REVERT: 2 12 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8158 (tpp-160) REVERT: 2 16 HIS cc_start: 0.7332 (m-70) cc_final: 0.7085 (m170) REVERT: Z 22 THR cc_start: 0.8876 (m) cc_final: 0.8640 (p) REVERT: Z 37 ARG cc_start: 0.6751 (mmt-90) cc_final: 0.6439 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.5117 time to fit residues: 269.8932 Evaluate side-chains 213 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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: 9.9990 chunk 265 optimal weight: 7.9990 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: 5.9990 chunk 106 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 204 optimal weight: 0.0980 chunk 317 optimal weight: 1.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- 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** 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 T 70 HIS T 92 ASN 0 3 GLN 2 16 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 58472 Z= 0.276 Angle : 0.580 10.852 88261 Z= 0.291 Chirality : 0.031 0.245 11427 Planarity : 0.005 0.051 4167 Dihedral : 23.309 179.150 30992 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 2.16 % Allowed : 10.81 % Favored : 87.03 % 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: -0.14 (0.20), residues: 1660 helix: 0.80 (0.23), residues: 513 sheet: 0.34 (0.31), residues: 264 loop : -0.73 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 78 HIS 0.013 0.002 HIS R 82 PHE 0.011 0.002 PHE E 19 TYR 0.015 0.002 TYR Q 46 ARG 0.022 0.001 ARG Y 7 *********************** 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 270 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 126 ARG cc_start: 0.1898 (mtm180) cc_final: 0.0825 (ttp80) REVERT: N 1 MET cc_start: 0.7497 (ppp) cc_final: 0.7194 (pmm) REVERT: N 43 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8036 (mt-10) REVERT: N 106 ASP cc_start: 0.7860 (t0) cc_final: 0.7571 (t0) REVERT: P 14 GLN cc_start: 0.8242 (mp10) cc_final: 0.7854 (mm-40) REVERT: P 70 GLU cc_start: 0.7652 (pm20) cc_final: 0.7400 (pm20) REVERT: S 110 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: T 79 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8059 (p0) outliers start: 30 outliers final: 18 residues processed: 254 average time/residue: 0.5426 time to fit residues: 232.0337 Evaluate side-chains 226 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain Z residue 23 LEU 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: 3.9990 chunk 216 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 58472 Z= 0.237 Angle : 0.542 9.279 88261 Z= 0.274 Chirality : 0.031 0.214 11427 Planarity : 0.004 0.042 4167 Dihedral : 23.420 179.026 30992 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.88 % Allowed : 13.54 % Favored : 83.57 % 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: -0.49 (0.20), residues: 1660 helix: 0.39 (0.23), residues: 519 sheet: 0.07 (0.30), residues: 278 loop : -0.87 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 78 HIS 0.012 0.002 HIS R 82 PHE 0.010 0.001 PHE Q 100 TYR 0.013 0.002 TYR J 75 ARG 0.007 0.001 ARG 2 12 *********************** 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 274 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 234 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8568 (m100) cc_final: 0.7700 (m100) REVERT: K 1 MET cc_start: 0.7028 (tpp) cc_final: 0.6721 (mmm) REVERT: K 80 ASP cc_start: 0.6725 (m-30) cc_final: 0.6066 (t0) REVERT: L 18 ARG cc_start: 0.7668 (mtp180) cc_final: 0.6876 (mtp180) REVERT: L 126 ARG cc_start: 0.2028 (mtm180) cc_final: 0.1101 (ttt90) REVERT: N 106 ASP cc_start: 0.7895 (t0) cc_final: 0.7578 (t0) REVERT: P 101 GLU cc_start: 0.6985 (pp20) cc_final: 0.6692 (pp20) REVERT: Q 10 ARG cc_start: 0.8285 (tpp80) cc_final: 0.7917 (tpp80) REVERT: S 11 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6864 (mtp180) REVERT: T 79 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8039 (p0) REVERT: Y 27 ASN cc_start: 0.8383 (m-40) cc_final: 0.8143 (m-40) REVERT: 0 11 LYS cc_start: 0.9049 (tppp) cc_final: 0.8699 (tppt) outliers start: 40 outliers final: 29 residues processed: 252 average time/residue: 0.5560 time to fit residues: 238.3763 Evaluate side-chains 243 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL 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: 9.9990 chunk 165 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 213 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 chunk 338 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 58472 Z= 0.333 Angle : 0.634 10.944 88261 Z= 0.320 Chirality : 0.035 0.231 11427 Planarity : 0.005 0.046 4167 Dihedral : 23.623 179.720 30992 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.11 % Allowed : 14.84 % Favored : 81.05 % 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: -0.79 (0.20), residues: 1660 helix: 0.12 (0.23), residues: 516 sheet: -0.17 (0.31), residues: 275 loop : -0.99 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 78 HIS 0.015 0.002 HIS R 82 PHE 0.014 0.002 PHE S 75 TYR 0.012 0.002 TYR S 38 ARG 0.006 0.001 ARG T 12 *********************** 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 283 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8661 (m100) cc_final: 0.7868 (m100) REVERT: J 49 ASP cc_start: 0.8460 (t70) cc_final: 0.8168 (t70) REVERT: N 106 ASP cc_start: 0.7759 (t0) cc_final: 0.7458 (t0) REVERT: N 110 MET cc_start: 0.7802 (ttt) cc_final: 0.7438 (ttt) REVERT: P 74 GLN cc_start: 0.8584 (mp10) cc_final: 0.8308 (mp10) REVERT: P 101 GLU cc_start: 0.7051 (pp20) cc_final: 0.6685 (pp20) REVERT: R 37 GLU cc_start: 0.8260 (pm20) cc_final: 0.7842 (pm20) REVERT: T 79 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8000 (p0) REVERT: 0 3 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6013 (pt0) REVERT: 2 12 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8467 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8826 (mtt90) cc_final: 0.8373 (mtt90) REVERT: Z 46 MET cc_start: 0.5991 (mmm) cc_final: 0.5790 (mmm) outliers start: 57 outliers final: 38 residues processed: 260 average time/residue: 0.5261 time to fit residues: 231.4522 Evaluate side-chains 247 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 303 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 58472 Z= 0.335 Angle : 0.650 10.585 88261 Z= 0.329 Chirality : 0.036 0.257 11427 Planarity : 0.005 0.053 4167 Dihedral : 23.784 178.395 30992 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.18 % Allowed : 16.35 % Favored : 79.47 % 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: -1.14 (0.20), residues: 1660 helix: -0.15 (0.22), residues: 512 sheet: -0.69 (0.30), residues: 275 loop : -1.11 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP T 80 HIS 0.016 0.002 HIS R 82 PHE 0.030 0.002 PHE Y 26 TYR 0.018 0.002 TYR J 125 ARG 0.008 0.001 ARG K 78 *********************** 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 281 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 223 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8754 (m100) cc_final: 0.7872 (m100) REVERT: J 49 ASP cc_start: 0.8548 (t70) cc_final: 0.8264 (t70) REVERT: K 7 MET cc_start: 0.8510 (tpt) cc_final: 0.8226 (tpp) REVERT: L 78 ARG cc_start: 0.7056 (mtt-85) cc_final: 0.6799 (mtt-85) REVERT: N 113 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9121 (pt) REVERT: R 37 GLU cc_start: 0.8197 (pm20) cc_final: 0.7900 (pm20) REVERT: S 65 ASP cc_start: 0.6952 (t0) cc_final: 0.6556 (t0) REVERT: S 68 ASP cc_start: 0.8049 (p0) cc_final: 0.7459 (p0) REVERT: T 79 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8004 (p0) REVERT: 0 3 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5910 (pt0) REVERT: 2 12 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8280 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8756 (mtt90) cc_final: 0.8364 (mtt90) REVERT: Z 18 LYS cc_start: 0.9148 (tptt) cc_final: 0.8903 (tptt) REVERT: Z 26 LEU cc_start: 0.9054 (mm) cc_final: 0.8744 (mp) REVERT: Z 46 MET cc_start: 0.6586 (mmm) cc_final: 0.6382 (mmm) outliers start: 58 outliers final: 45 residues processed: 255 average time/residue: 0.5199 time to fit residues: 226.2532 Evaluate side-chains 253 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL 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: 6.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 281 optimal weight: 0.7980 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: 7.5590 ------------------------------------------------------------------------------- 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** K 13 ASN ** 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 58472 Z= 0.370 Angle : 0.684 11.407 88261 Z= 0.345 Chirality : 0.037 0.251 11427 Planarity : 0.005 0.049 4167 Dihedral : 23.866 178.629 30992 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.76 % Allowed : 16.21 % Favored : 79.03 % 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: -1.32 (0.20), residues: 1660 helix: -0.25 (0.22), residues: 515 sheet: -0.71 (0.31), residues: 272 loop : -1.29 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.015 0.002 HIS R 82 PHE 0.022 0.002 PHE Y 26 TYR 0.015 0.002 TYR S 38 ARG 0.008 0.001 ARG E 40 *********************** 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 280 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 214 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7191 (t70) REVERT: E 78 TRP cc_start: 0.8746 (m100) cc_final: 0.7739 (m100) REVERT: J 49 ASP cc_start: 0.8526 (t70) cc_final: 0.8211 (t70) REVERT: L 78 ARG cc_start: 0.7200 (mtt-85) cc_final: 0.6924 (mtt-85) REVERT: R 37 GLU cc_start: 0.8183 (pm20) cc_final: 0.7972 (pm20) REVERT: R 45 GLU cc_start: 0.8765 (pm20) cc_final: 0.8393 (pm20) REVERT: 0 3 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.5998 (pt0) REVERT: 2 12 ARG cc_start: 0.8919 (tpp80) cc_final: 0.8296 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8730 (mtt90) cc_final: 0.8390 (mtt90) REVERT: Z 18 LYS cc_start: 0.8761 (tptt) cc_final: 0.8555 (tptt) outliers start: 66 outliers final: 53 residues processed: 252 average time/residue: 0.5253 time to fit residues: 225.1493 Evaluate side-chains 253 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.5980 chunk 38 optimal weight: 40.0000 chunk 192 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** K 88 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN Y 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 58472 Z= 0.169 Angle : 0.538 11.402 88261 Z= 0.273 Chirality : 0.031 0.216 11427 Planarity : 0.004 0.065 4167 Dihedral : 23.714 178.281 30992 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.17 % Allowed : 18.52 % Favored : 78.31 % 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: -0.93 (0.20), residues: 1660 helix: 0.14 (0.23), residues: 512 sheet: -0.48 (0.32), residues: 273 loop : -1.09 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 78 HIS 0.006 0.001 HIS 2 16 PHE 0.010 0.001 PHE N 21 TYR 0.015 0.001 TYR J 125 ARG 0.010 0.000 ARG Z 44 *********************** 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 274 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8600 (m100) cc_final: 0.7611 (m100) REVERT: J 49 ASP cc_start: 0.8425 (t70) cc_final: 0.8040 (t70) REVERT: L 78 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6962 (mtt-85) REVERT: L 96 LYS cc_start: 0.2693 (mptt) cc_final: 0.2248 (mptt) REVERT: P 101 GLU cc_start: 0.7113 (pp20) cc_final: 0.6613 (pp20) REVERT: R 45 GLU cc_start: 0.8682 (pm20) cc_final: 0.8405 (pm20) REVERT: T 79 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8039 (p0) REVERT: 2 12 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8095 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8261 (mtt90) REVERT: Z 26 LEU cc_start: 0.9054 (mm) cc_final: 0.8776 (mp) outliers start: 44 outliers final: 33 residues processed: 255 average time/residue: 0.5152 time to fit residues: 223.9618 Evaluate side-chains 242 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 0.5980 chunk 229 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 overall best weight: 6.5192 ------------------------------------------------------------------------------- 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** 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: 0.8142 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 58472 Z= 0.326 Angle : 0.639 10.888 88261 Z= 0.322 Chirality : 0.035 0.239 11427 Planarity : 0.005 0.048 4167 Dihedral : 23.738 179.138 30992 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.53 % Allowed : 19.31 % Favored : 77.16 % 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: -1.13 (0.20), residues: 1660 helix: 0.03 (0.23), residues: 514 sheet: -0.62 (0.32), residues: 266 loop : -1.24 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.007 0.002 HIS R 12 PHE 0.028 0.002 PHE Y 26 TYR 0.016 0.002 TYR S 38 ARG 0.009 0.001 ARG Y 7 *********************** 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 259 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6990 (t70) REVERT: E 78 TRP cc_start: 0.8733 (m100) cc_final: 0.7731 (m100) REVERT: J 49 ASP cc_start: 0.8594 (t70) cc_final: 0.8284 (t70) REVERT: L 78 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6921 (mtt-85) REVERT: N 113 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9135 (pt) REVERT: R 45 GLU cc_start: 0.8710 (pm20) cc_final: 0.8434 (pm20) REVERT: S 13 SER cc_start: 0.9581 (t) cc_final: 0.9114 (p) REVERT: S 110 ARG cc_start: 0.8366 (tpp-160) cc_final: 0.8065 (tpp-160) REVERT: T 79 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8097 (p0) REVERT: 0 3 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.5946 (pt0) REVERT: 2 12 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8172 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8713 (mtt90) cc_final: 0.8369 (mtt90) REVERT: Z 26 LEU cc_start: 0.9060 (mm) cc_final: 0.8782 (mp) outliers start: 49 outliers final: 39 residues processed: 238 average time/residue: 0.5271 time to fit residues: 214.4558 Evaluate side-chains 245 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 297 optimal weight: 6.9990 chunk 313 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 58472 Z= 0.197 Angle : 0.556 12.221 88261 Z= 0.281 Chirality : 0.031 0.265 11427 Planarity : 0.004 0.047 4167 Dihedral : 23.691 179.167 30992 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.17 % Allowed : 20.24 % Favored : 76.59 % 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: -1.00 (0.20), residues: 1660 helix: 0.16 (0.23), residues: 515 sheet: -0.58 (0.32), residues: 267 loop : -1.17 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 78 HIS 0.004 0.001 HIS S 7 PHE 0.026 0.001 PHE Y 26 TYR 0.012 0.002 TYR J 125 ARG 0.007 0.000 ARG Y 29 *********************** 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 265 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 ASP cc_start: 0.8496 (t70) cc_final: 0.8087 (t70) REVERT: L 96 LYS cc_start: 0.2794 (mptt) cc_final: 0.2298 (mptt) REVERT: N 118 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5099 (ttm110) REVERT: R 45 GLU cc_start: 0.8685 (pm20) cc_final: 0.8425 (pm20) REVERT: S 13 SER cc_start: 0.9501 (t) cc_final: 0.9186 (p) REVERT: T 79 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8065 (p0) REVERT: 0 3 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5840 (pt0) REVERT: 2 12 ARG cc_start: 0.8924 (tpp80) cc_final: 0.8502 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8329 (mtt90) REVERT: Z 26 LEU cc_start: 0.9018 (mm) cc_final: 0.8712 (mp) outliers start: 44 outliers final: 35 residues processed: 247 average time/residue: 0.5221 time to fit residues: 221.0989 Evaluate side-chains 252 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 34 SER Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 348 optimal weight: 0.2980 chunk 320 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 28 optimal weight: 30.0000 chunk 214 optimal weight: 0.3980 chunk 170 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 58472 Z= 0.193 Angle : 0.554 12.826 88261 Z= 0.280 Chirality : 0.031 0.274 11427 Planarity : 0.004 0.048 4167 Dihedral : 23.682 179.486 30992 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.88 % Allowed : 20.53 % Favored : 76.59 % 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: -0.96 (0.21), residues: 1660 helix: 0.19 (0.23), residues: 515 sheet: -0.54 (0.32), residues: 267 loop : -1.15 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 78 HIS 0.005 0.001 HIS 2 16 PHE 0.019 0.001 PHE Y 26 TYR 0.013 0.002 TYR S 38 ARG 0.004 0.000 ARG Q 50 ********************** 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 258 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 218 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 11 MET cc_start: 0.6928 (ptm) cc_final: 0.6699 (ppp) REVERT: J 49 ASP cc_start: 0.8486 (t70) cc_final: 0.8165 (t70) REVERT: J 114 LEU cc_start: 0.8993 (tp) cc_final: 0.8791 (tp) REVERT: J 118 MET cc_start: 0.8595 (mmt) cc_final: 0.8101 (mmm) REVERT: L 96 LYS cc_start: 0.2799 (mptt) cc_final: 0.2291 (mptt) REVERT: N 118 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.4987 (ttm110) REVERT: R 45 GLU cc_start: 0.8671 (pm20) cc_final: 0.8408 (pm20) REVERT: S 13 SER cc_start: 0.9494 (t) cc_final: 0.9215 (p) REVERT: T 79 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8071 (p0) REVERT: 0 3 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5779 (pt0) REVERT: 2 12 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8493 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8321 (mtt90) REVERT: Z 26 LEU cc_start: 0.9002 (mm) cc_final: 0.8697 (mp) outliers start: 40 outliers final: 36 residues processed: 242 average time/residue: 0.5067 time to fit residues: 209.4545 Evaluate side-chains 254 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 40 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 285 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.072929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.050943 restraints weight = 306523.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052201 restraints weight = 126811.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.052965 restraints weight = 84274.989| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 58472 Z= 0.355 Angle : 0.675 12.345 88261 Z= 0.339 Chirality : 0.036 0.237 11427 Planarity : 0.005 0.107 4167 Dihedral : 23.831 179.708 30992 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.24 % Allowed : 20.53 % Favored : 76.22 % 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: -0.10 (0.23), residues: 514 sheet: -0.83 (0.31), residues: 277 loop : -1.29 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 60 HIS 0.008 0.002 HIS S 7 PHE 0.027 0.002 PHE Y 26 TYR 0.014 0.002 TYR T 84 ARG 0.008 0.001 ARG Y 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6117.41 seconds wall clock time: 112 minutes 37.29 seconds (6757.29 seconds total)