Starting phenix.real_space_refine on Thu Sep 26 04:12:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc6_4381/09_2024/6gc6_4381.cif" } resolution = 4.3 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= 0.070 sd= 0.487 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 2092 5.49 5 S 47 5.16 5 C 30355 2.51 5 N 11491 2.21 5 O 17419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61404 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 44960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2092, 44960 Classifications: {'RNA': 2092} Modifications used: {'rna2p_pur': 206, 'rna2p_pyr': 111, 'rna3p_pur': 1025, 'rna3p_pyr': 750} Link IDs: {'rna2p': 317, 'rna3p': 1774} Chain breaks: 6 Chain: "C" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1561 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1366 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 1 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 26.58, per 1000 atoms: 0.43 Number of scatterers: 61404 At special positions: 0 Unit cell: (209.56, 166.16, 223.2, 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 47 16.00 P 2092 15.00 O 17419 8.00 N 11491 7.00 C 30355 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: 11.10 Conformation dependent library (CDL) restraints added in 2.8 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 29 sheets defined 27.4% alpha, 20.1% beta 599 base pairs and 1090 stacking pairs defined. Time for finding SS restraints: 24.81 Creating SS restraints... Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.017A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'D' and resid 61 through 72 removed outlier: 4.026A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.510A pdb=" N VAL E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.740A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.159A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 80 removed outlier: 4.625A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.549A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.717A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.678A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.475A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.671A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.585A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.862A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.331A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 130 through 135' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.944A pdb=" N ARG N 17 " --> pdb=" O ASN N 13 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.195A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 67 removed outlier: 3.799A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU N 65 " --> pdb=" O ALA N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.666A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.914A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) No H-bonds generated for '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: 3.704A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.612A pdb=" N ALA P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 18 removed outlier: 3.921A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 4.052A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.048A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.597A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP Q 101 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.720A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.694A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.457A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 removed outlier: 3.647A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 9 removed outlier: 3.771A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.528A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 32 removed outlier: 3.819A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.199A 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 23 Processing helix chain '2' and resid 26 through 38 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.887A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.132A pdb=" N VAL C 3 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 17 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.591A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 130 removed outlier: 7.468A pdb=" N ARG C 188 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL C 143 " --> pdb=" O ARG C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.780A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL C 164 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.749A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 25 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 38 removed outlier: 3.861A pdb=" N ARG D 33 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 120 removed outlier: 7.007A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 8 through 9 removed outlier: 4.291A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 23 through 25 Processing sheet with id=AB1, first strand: chain 'G' and resid 82 through 87 Processing sheet with id=AB2, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.897A pdb=" N LEU G 104 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.650A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AB5, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.728A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.523A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.523A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.606A pdb=" N ILE N 34 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'R' and resid 19 through 22 removed outlier: 3.566A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP R 95 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.967A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 3 through 8 removed outlier: 6.869A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 82 through 87 removed outlier: 3.845A pdb=" N ARG S 84 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 96 " --> pdb=" O ARG S 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.726A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 63 through 65 removed outlier: 6.134A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE U 11 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA U 70 " --> pdb=" O ILE U 11 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.689A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 83 through 87 removed outlier: 3.839A pdb=" N GLY U 83 " --> pdb=" O PHE U 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE U 94 " --> pdb=" O GLY U 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS U 90 " --> pdb=" O GLU U 87 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AD1, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AD2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.575A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1503 hydrogen bonds 2356 hydrogen bond angles 0 basepair planarities 599 basepair parallelities 1090 stacking parallelities Total time for adding SS restraints: 71.00 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8552 1.33 - 1.45: 28364 1.45 - 1.57: 25831 1.57 - 1.69: 4177 1.69 - 1.81: 88 Bond restraints: 67012 Sorted by residual: bond pdb=" C ILE K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.30e-02 5.92e+03 5.79e+00 bond pdb=" CA ASN U 98 " pdb=" CB ASN U 98 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.33e-02 5.65e+03 5.50e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.20e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.14e+00 bond pdb=" C3' G A 271 " pdb=" O3' G A 271 " ideal model delta sigma weight residual 1.427 1.455 -0.028 1.50e-02 4.44e+03 3.55e+00 ... (remaining 67007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 99614 2.40 - 4.81: 1142 4.81 - 7.21: 111 7.21 - 9.61: 21 9.61 - 12.01: 5 Bond angle restraints: 100893 Sorted by residual: angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.46e+01 angle pdb=" N VAL D 98 " pdb=" CA VAL D 98 " pdb=" C VAL D 98 " ideal model delta sigma weight residual 112.83 107.10 5.73 9.90e-01 1.02e+00 3.35e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 124.82 134.79 -9.97 1.78e+00 3.16e-01 3.14e+01 angle pdb=" C VAL 0 53 " pdb=" N ILE 0 54 " pdb=" CA ILE 0 54 " ideal model delta sigma weight residual 120.77 127.99 -7.22 1.31e+00 5.83e-01 3.04e+01 angle pdb=" C ASP S 65 " pdb=" N ILE S 66 " pdb=" CA ILE S 66 " ideal model delta sigma weight residual 120.46 127.36 -6.90 1.37e+00 5.33e-01 2.54e+01 ... (remaining 100888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 37705 35.30 - 70.60: 4543 70.60 - 105.90: 542 105.90 - 141.20: 2 141.20 - 176.50: 6 Dihedral angle restraints: 42798 sinusoidal: 36792 harmonic: 6006 Sorted by residual: dihedral pdb=" CA GLY C 11 " pdb=" C GLY C 11 " pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta harmonic sigma weight residual -180.00 -129.02 -50.98 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 46.03 153.97 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 61.18 138.82 1 1.50e+01 4.44e-03 7.48e+01 ... (remaining 42795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 12060 0.057 - 0.113: 803 0.113 - 0.170: 122 0.170 - 0.227: 16 0.227 - 0.284: 4 Chirality restraints: 13005 Sorted by residual: chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' A A1378 " pdb=" C4' A A1378 " pdb=" O3' A A1378 " pdb=" C2' A A1378 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASN U 98 " pdb=" N ASN U 98 " pdb=" C ASN U 98 " pdb=" CB ASN U 98 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 13002 not shown) Planarity restraints: 4966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 110 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C VAL L 110 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL L 110 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE L 111 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 11 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C GLY C 11 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY C 11 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG C 12 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1736 " -0.029 2.00e-02 2.50e+03 1.63e-02 5.97e+00 pdb=" N1 U A1736 " 0.037 2.00e-02 2.50e+03 pdb=" C2 U A1736 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U A1736 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A1736 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A1736 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U A1736 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U A1736 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A1736 " 0.004 2.00e-02 2.50e+03 ... (remaining 4963 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 9744 2.76 - 3.30: 49531 3.30 - 3.83: 127930 3.83 - 4.37: 148474 4.37 - 4.90: 199079 Nonbonded interactions: 534758 Sorted by model distance: nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 2.229 3.040 nonbonded pdb=" O2 C A 269 " pdb=" N2 G A 370 " model vdw 2.230 2.496 nonbonded pdb=" O2' C A 239 " pdb=" O2' G A 622 " model vdw 2.257 3.040 nonbonded pdb=" O ILE S 35 " pdb=" OG1 THR S 39 " model vdw 2.273 3.040 nonbonded pdb=" O LEU S 33 " pdb=" OG1 THR S 37 " model vdw 2.281 3.040 ... (remaining 534753 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.850 Check model and map are aligned: 0.370 Set scattering table: 0.430 Process input model: 165.980 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.170 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 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 : 0.003 0.051 67012 Z= 0.160 Angle : 0.662 12.014 100893 Z= 0.339 Chirality : 0.031 0.284 13005 Planarity : 0.005 0.053 4966 Dihedral : 22.325 176.501 38926 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.14), residues: 2076 helix: -4.21 (0.10), residues: 514 sheet: -1.27 (0.27), residues: 339 loop : -2.34 (0.14), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 60 HIS 0.006 0.001 HIS R 82 PHE 0.016 0.002 PHE R 5 TYR 0.013 0.001 TYR Q 24 ARG 0.007 0.001 ARG R 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 LEU cc_start: 0.4040 (mt) cc_final: 0.3759 (mt) REVERT: G 74 MET cc_start: 0.0153 (mtt) cc_final: -0.0828 (ptm) REVERT: J 93 ILE cc_start: 0.7287 (mm) cc_final: 0.6840 (tp) REVERT: J 101 ILE cc_start: 0.7570 (mm) cc_final: 0.7190 (mm) REVERT: J 114 LEU cc_start: 0.7468 (tp) cc_final: 0.7229 (tt) REVERT: K 73 ASP cc_start: 0.5516 (p0) cc_final: 0.5237 (p0) REVERT: N 28 LEU cc_start: 0.6479 (tp) cc_final: 0.6224 (tp) REVERT: N 53 THR cc_start: 0.7507 (m) cc_final: 0.6363 (m) REVERT: N 57 THR cc_start: 0.7554 (m) cc_final: 0.7082 (m) REVERT: N 65 LEU cc_start: 0.7373 (tp) cc_final: 0.7085 (tp) REVERT: Q 90 ASP cc_start: 0.7017 (p0) cc_final: 0.6365 (p0) REVERT: R 63 VAL cc_start: 0.6919 (t) cc_final: 0.6336 (t) REVERT: S 30 SER cc_start: 0.7783 (m) cc_final: 0.6969 (t) REVERT: S 72 THR cc_start: 0.6664 (p) cc_final: 0.6380 (t) REVERT: S 75 PHE cc_start: 0.6629 (p90) cc_final: 0.6428 (p90) REVERT: S 76 VAL cc_start: 0.8409 (t) cc_final: 0.7799 (t) REVERT: S 106 VAL cc_start: 0.7238 (t) cc_final: 0.6796 (t) REVERT: T 50 LEU cc_start: 0.7468 (mp) cc_final: 0.7242 (mt) REVERT: U 30 SER cc_start: 0.6945 (p) cc_final: 0.6737 (m) REVERT: U 34 ILE cc_start: 0.6997 (mm) cc_final: 0.6365 (mm) REVERT: Z 13 ILE cc_start: 0.6604 (mt) cc_final: 0.6255 (mm) REVERT: Z 26 LEU cc_start: 0.7239 (mt) cc_final: 0.5870 (mt) outliers start: 0 outliers final: 0 residues processed: 851 average time/residue: 0.7068 time to fit residues: 946.0468 Evaluate side-chains 500 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 8.9990 chunk 313 optimal weight: 30.0000 chunk 174 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 0.0870 chunk 167 optimal weight: 30.0000 chunk 324 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 375 optimal weight: 8.9990 overall best weight: 7.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 116 GLN C 199 HIS ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN L 4 ASN N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 ASN S 7 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN U 65 GLN U 68 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 67012 Z= 0.325 Angle : 0.718 13.703 100893 Z= 0.366 Chirality : 0.037 0.374 13005 Planarity : 0.006 0.099 4966 Dihedral : 23.502 173.636 34819 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 0.12 % Allowed : 3.96 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.16), residues: 2076 helix: -1.98 (0.19), residues: 543 sheet: -0.87 (0.27), residues: 344 loop : -1.99 (0.15), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP R 92 HIS 0.012 0.002 HIS T 70 PHE 0.027 0.003 PHE S 75 TYR 0.025 0.002 TYR Q 44 ARG 0.038 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 569 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 108 ASP cc_start: 0.5114 (t0) cc_final: 0.4886 (t0) REVERT: E 30 GLN cc_start: 0.5883 (tp-100) cc_final: 0.5540 (tp-100) REVERT: E 43 THR cc_start: 0.6875 (p) cc_final: 0.6379 (p) REVERT: G 74 MET cc_start: 0.0351 (mtt) cc_final: -0.0314 (ttp) REVERT: J 93 ILE cc_start: 0.7128 (mm) cc_final: 0.6857 (tp) REVERT: K 47 ILE cc_start: 0.6223 (pt) cc_final: 0.5984 (pt) REVERT: K 73 ASP cc_start: 0.5987 (p0) cc_final: 0.5742 (p0) REVERT: L 3 LEU cc_start: 0.7134 (mm) cc_final: 0.6871 (mm) REVERT: N 57 THR cc_start: 0.7828 (m) cc_final: 0.7527 (m) REVERT: N 81 ASN cc_start: 0.7730 (p0) cc_final: 0.6964 (p0) REVERT: S 30 SER cc_start: 0.7438 (m) cc_final: 0.7117 (t) REVERT: S 37 THR cc_start: 0.8528 (m) cc_final: 0.8321 (m) REVERT: S 61 ASN cc_start: 0.6348 (m110) cc_final: 0.5622 (m110) REVERT: S 69 LEU cc_start: 0.6492 (mm) cc_final: 0.6278 (mm) REVERT: T 1 MET cc_start: 0.2142 (mtt) cc_final: 0.1877 (mtt) REVERT: T 50 LEU cc_start: 0.7182 (mp) cc_final: 0.6923 (mm) REVERT: U 34 ILE cc_start: 0.7055 (mm) cc_final: 0.6225 (mm) REVERT: 0 9 ARG cc_start: 0.6431 (mtt180) cc_final: 0.6211 (mtt180) outliers start: 2 outliers final: 1 residues processed: 570 average time/residue: 0.6736 time to fit residues: 622.5003 Evaluate side-chains 437 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 376 optimal weight: 8.9990 chunk 406 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 76 HIS J 86 GLN K 93 GLN N 3 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Q 80 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 2 6 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 67012 Z= 0.253 Angle : 0.614 9.174 100893 Z= 0.317 Chirality : 0.034 0.240 13005 Planarity : 0.006 0.102 4966 Dihedral : 23.552 174.468 34819 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.17), residues: 2076 helix: -1.39 (0.20), residues: 538 sheet: -0.60 (0.26), residues: 377 loop : -1.78 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 15 HIS 0.010 0.002 HIS C 199 PHE 0.019 0.002 PHE S 75 TYR 0.020 0.002 TYR D 45 ARG 0.013 0.001 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 527 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LEU cc_start: 0.7440 (pp) cc_final: 0.7025 (pt) REVERT: D 108 ASP cc_start: 0.5150 (t0) cc_final: 0.4885 (t0) REVERT: D 183 GLU cc_start: 0.7995 (pp20) cc_final: 0.7756 (pp20) REVERT: E 43 THR cc_start: 0.6967 (p) cc_final: 0.6496 (p) REVERT: G 74 MET cc_start: 0.0919 (mtt) cc_final: 0.0418 (mtm) REVERT: J 93 ILE cc_start: 0.7046 (mm) cc_final: 0.6751 (tp) REVERT: J 101 ILE cc_start: 0.7616 (tp) cc_final: 0.7255 (tp) REVERT: K 8 LEU cc_start: 0.7292 (mm) cc_final: 0.7016 (mm) REVERT: K 73 ASP cc_start: 0.6474 (p0) cc_final: 0.5892 (p0) REVERT: N 20 MET cc_start: 0.6593 (tpp) cc_final: 0.6265 (tpp) REVERT: N 24 MET cc_start: 0.6590 (mmt) cc_final: 0.6321 (mmt) REVERT: N 53 THR cc_start: 0.8530 (m) cc_final: 0.7980 (m) REVERT: N 57 THR cc_start: 0.8186 (m) cc_final: 0.7853 (m) REVERT: N 81 ASN cc_start: 0.7828 (p0) cc_final: 0.7237 (p0) REVERT: Q 90 ASP cc_start: 0.7054 (p0) cc_final: 0.6736 (p0) REVERT: S 30 SER cc_start: 0.7373 (m) cc_final: 0.6808 (t) REVERT: S 51 LEU cc_start: 0.7880 (pp) cc_final: 0.7658 (pp) REVERT: S 106 VAL cc_start: 0.7429 (t) cc_final: 0.7074 (t) REVERT: T 50 LEU cc_start: 0.7597 (mp) cc_final: 0.7299 (mm) REVERT: U 58 VAL cc_start: 0.6538 (t) cc_final: 0.6325 (t) REVERT: 0 18 HIS cc_start: 0.6813 (m90) cc_final: 0.6515 (m-70) REVERT: Z 55 LYS cc_start: 0.5716 (mmtm) cc_final: 0.5489 (mmtm) outliers start: 1 outliers final: 1 residues processed: 528 average time/residue: 0.6575 time to fit residues: 567.7299 Evaluate side-chains 417 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 416 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 10.0000 chunk 283 optimal weight: 40.0000 chunk 195 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 377 optimal weight: 9.9990 chunk 400 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 358 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 59 GLN C 85 ASN C 114 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 67012 Z= 0.365 Angle : 0.777 10.453 100893 Z= 0.400 Chirality : 0.041 0.247 13005 Planarity : 0.007 0.088 4966 Dihedral : 24.015 169.099 34819 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 28.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.38 % Favored : 91.57 % Rotamer: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2076 helix: -1.66 (0.20), residues: 547 sheet: -0.99 (0.26), residues: 396 loop : -1.82 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J 15 HIS 0.010 0.003 HIS 0 37 PHE 0.027 0.003 PHE L 107 TYR 0.021 0.002 TYR N 94 ARG 0.009 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 507 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LEU cc_start: 0.7559 (pp) cc_final: 0.7181 (pp) REVERT: D 18 ASP cc_start: 0.7585 (p0) cc_final: 0.7224 (p0) REVERT: K 1 MET cc_start: 0.5272 (pmm) cc_final: 0.5051 (pmm) REVERT: K 39 ILE cc_start: 0.7149 (pt) cc_final: 0.6841 (mm) REVERT: K 73 ASP cc_start: 0.6817 (p0) cc_final: 0.6450 (p0) REVERT: P 3 ILE cc_start: 0.7835 (pt) cc_final: 0.7592 (pt) REVERT: P 5 LYS cc_start: 0.7378 (mttm) cc_final: 0.6978 (mttm) REVERT: Q 48 ASP cc_start: 0.6842 (m-30) cc_final: 0.6078 (m-30) REVERT: Q 90 ASP cc_start: 0.7146 (p0) cc_final: 0.6834 (p0) REVERT: R 39 LEU cc_start: 0.8315 (mp) cc_final: 0.7896 (mp) REVERT: S 51 LEU cc_start: 0.7833 (pp) cc_final: 0.7611 (pp) REVERT: Y 1 MET cc_start: 0.5622 (ppp) cc_final: 0.5210 (ppp) REVERT: 0 3 GLN cc_start: 0.6655 (mp-120) cc_final: 0.6365 (mt0) REVERT: 0 18 HIS cc_start: 0.7208 (m90) cc_final: 0.6433 (m-70) outliers start: 2 outliers final: 1 residues processed: 509 average time/residue: 0.6487 time to fit residues: 541.4798 Evaluate side-chains 391 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 0.5980 chunk 165 optimal weight: 50.0000 chunk 341 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 359 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 67012 Z= 0.176 Angle : 0.565 10.344 100893 Z= 0.293 Chirality : 0.033 0.252 13005 Planarity : 0.004 0.048 4966 Dihedral : 23.721 172.838 34819 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2076 helix: -1.17 (0.21), residues: 547 sheet: -0.77 (0.25), residues: 402 loop : -1.65 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 15 HIS 0.005 0.001 HIS E 92 PHE 0.016 0.002 PHE S 75 TYR 0.014 0.001 TYR N 112 ARG 0.006 0.001 ARG N 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 513 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 MET cc_start: 0.3643 (mmp) cc_final: 0.3235 (tpt) REVERT: D 108 ASP cc_start: 0.6058 (t0) cc_final: 0.5833 (t0) REVERT: D 183 GLU cc_start: 0.8242 (pp20) cc_final: 0.7951 (pp20) REVERT: J 69 ARG cc_start: 0.5315 (tpp80) cc_final: 0.4997 (tpp80) REVERT: K 73 ASP cc_start: 0.6331 (p0) cc_final: 0.5991 (p0) REVERT: N 20 MET cc_start: 0.6500 (tpp) cc_final: 0.6210 (tpp) REVERT: N 53 THR cc_start: 0.8706 (p) cc_final: 0.8376 (t) REVERT: N 107 ASN cc_start: 0.7071 (t0) cc_final: 0.6834 (t0) REVERT: P 3 ILE cc_start: 0.7448 (pt) cc_final: 0.7211 (pt) REVERT: P 5 LYS cc_start: 0.7580 (mttm) cc_final: 0.6988 (mttm) REVERT: Q 116 LEU cc_start: 0.6487 (tt) cc_final: 0.5998 (tt) REVERT: S 24 ILE cc_start: 0.8962 (mm) cc_final: 0.8672 (mm) REVERT: T 56 GLU cc_start: 0.6486 (pp20) cc_final: 0.6277 (tm-30) REVERT: Y 8 GLU cc_start: 0.5815 (tt0) cc_final: 0.5505 (tt0) REVERT: 0 3 GLN cc_start: 0.6715 (mp-120) cc_final: 0.6351 (mt0) REVERT: 0 18 HIS cc_start: 0.6844 (m90) cc_final: 0.6092 (m-70) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.6409 time to fit residues: 540.2116 Evaluate side-chains 394 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 10.0000 chunk 360 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 400 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 185 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 86 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 36 GLN Q 80 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 67012 Z= 0.346 Angle : 0.727 13.320 100893 Z= 0.372 Chirality : 0.040 0.251 13005 Planarity : 0.006 0.147 4966 Dihedral : 24.020 167.899 34819 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.06 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2076 helix: -1.39 (0.20), residues: 554 sheet: -1.02 (0.25), residues: 412 loop : -1.73 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 15 HIS 0.014 0.002 HIS C 24 PHE 0.022 0.003 PHE S 75 TYR 0.016 0.002 TYR N 112 ARG 0.026 0.001 ARG Y 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7807 (t0) cc_final: 0.7603 (t0) REVERT: D 18 ASP cc_start: 0.7339 (p0) cc_final: 0.7086 (p0) REVERT: D 90 PHE cc_start: 0.7413 (m-80) cc_final: 0.6956 (m-80) REVERT: D 99 GLU cc_start: 0.7281 (mp0) cc_final: 0.7074 (mp0) REVERT: D 183 GLU cc_start: 0.8391 (pp20) cc_final: 0.7909 (pp20) REVERT: J 122 LEU cc_start: 0.8240 (tp) cc_final: 0.7969 (tt) REVERT: J 136 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6724 (tm-30) REVERT: K 39 ILE cc_start: 0.7177 (pt) cc_final: 0.6965 (mm) REVERT: K 73 ASP cc_start: 0.6449 (p0) cc_final: 0.6163 (p0) REVERT: N 20 MET cc_start: 0.6871 (tpp) cc_final: 0.6659 (tpp) REVERT: N 53 THR cc_start: 0.8739 (p) cc_final: 0.8374 (t) REVERT: P 3 ILE cc_start: 0.7837 (pt) cc_final: 0.7579 (pt) REVERT: P 5 LYS cc_start: 0.7499 (mttm) cc_final: 0.7138 (mttm) REVERT: Q 63 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5262 (ttt180) REVERT: Q 89 ILE cc_start: 0.6925 (mm) cc_final: 0.6553 (mm) REVERT: Q 90 ASP cc_start: 0.6807 (p0) cc_final: 0.6597 (p0) REVERT: R 39 LEU cc_start: 0.7887 (tp) cc_final: 0.7516 (tp) REVERT: S 24 ILE cc_start: 0.9079 (mm) cc_final: 0.8842 (mm) REVERT: S 45 VAL cc_start: 0.7796 (t) cc_final: 0.7570 (p) REVERT: S 51 LEU cc_start: 0.7841 (pp) cc_final: 0.7585 (pp) REVERT: S 81 SER cc_start: 0.7722 (t) cc_final: 0.7178 (m) REVERT: S 95 ARG cc_start: 0.6226 (tmm160) cc_final: 0.5976 (ttp-170) REVERT: S 106 VAL cc_start: 0.7807 (t) cc_final: 0.7044 (t) REVERT: S 109 ASP cc_start: 0.7330 (p0) cc_final: 0.6917 (p0) REVERT: Y 8 GLU cc_start: 0.5785 (tt0) cc_final: 0.5349 (tt0) REVERT: Y 48 ARG cc_start: 0.7171 (mmp80) cc_final: 0.6682 (mmt-90) REVERT: 0 3 GLN cc_start: 0.6652 (mp-120) cc_final: 0.6196 (mt0) REVERT: 0 18 HIS cc_start: 0.7296 (m90) cc_final: 0.6612 (m-70) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.6203 time to fit residues: 508.5902 Evaluate side-chains 392 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 292 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 399 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 184 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 72 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 80 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.7753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 67012 Z= 0.277 Angle : 0.648 10.252 100893 Z= 0.335 Chirality : 0.037 0.263 13005 Planarity : 0.005 0.072 4966 Dihedral : 23.956 170.283 34819 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.14 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2076 helix: -1.21 (0.20), residues: 545 sheet: -0.97 (0.25), residues: 405 loop : -1.72 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP J 15 HIS 0.008 0.002 HIS C 24 PHE 0.021 0.002 PHE P 58 TYR 0.018 0.002 TYR J 16 ARG 0.010 0.001 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.7769 (t0) cc_final: 0.7516 (t0) REVERT: D 99 GLU cc_start: 0.7304 (mp0) cc_final: 0.7095 (mp0) REVERT: D 183 GLU cc_start: 0.8363 (pp20) cc_final: 0.7756 (pp20) REVERT: J 14 ASP cc_start: 0.5959 (p0) cc_final: 0.5706 (p0) REVERT: J 108 MET cc_start: 0.6758 (mmm) cc_final: 0.6287 (mmm) REVERT: K 1 MET cc_start: 0.5020 (pmm) cc_final: 0.4800 (pmm) REVERT: K 39 ILE cc_start: 0.7016 (pt) cc_final: 0.6635 (mm) REVERT: K 73 ASP cc_start: 0.6347 (p0) cc_final: 0.6027 (p0) REVERT: N 53 THR cc_start: 0.8708 (p) cc_final: 0.8382 (t) REVERT: N 54 LEU cc_start: 0.8077 (mt) cc_final: 0.7620 (mm) REVERT: N 107 ASN cc_start: 0.7488 (t0) cc_final: 0.7040 (t0) REVERT: P 3 ILE cc_start: 0.7746 (pt) cc_final: 0.7515 (pt) REVERT: P 5 LYS cc_start: 0.7433 (mttm) cc_final: 0.6959 (mttm) REVERT: Q 63 ARG cc_start: 0.5891 (mtt180) cc_final: 0.5651 (mtt180) REVERT: Q 89 ILE cc_start: 0.7025 (mm) cc_final: 0.6796 (mm) REVERT: Q 90 ASP cc_start: 0.6868 (p0) cc_final: 0.6661 (p0) REVERT: S 51 LEU cc_start: 0.7801 (pp) cc_final: 0.7562 (pp) REVERT: S 81 SER cc_start: 0.7644 (t) cc_final: 0.7299 (m) REVERT: Y 48 ARG cc_start: 0.7117 (mmp80) cc_final: 0.6911 (mmt-90) REVERT: 0 3 GLN cc_start: 0.6552 (mp-120) cc_final: 0.6239 (mt0) REVERT: 0 18 HIS cc_start: 0.7164 (m90) cc_final: 0.6696 (m90) REVERT: Z 13 ILE cc_start: 0.5165 (mt) cc_final: 0.4554 (tt) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.6401 time to fit residues: 537.3144 Evaluate side-chains 399 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 overall best weight: 7.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 86 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 80 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.8286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 67012 Z= 0.324 Angle : 0.718 12.298 100893 Z= 0.369 Chirality : 0.040 0.264 13005 Planarity : 0.006 0.062 4966 Dihedral : 24.102 167.730 34819 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 27.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.06 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2076 helix: -1.38 (0.20), residues: 548 sheet: -1.06 (0.25), residues: 407 loop : -1.76 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 15 HIS 0.010 0.002 HIS C 24 PHE 0.025 0.003 PHE R 5 TYR 0.019 0.002 TYR N 94 ARG 0.010 0.001 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ILE cc_start: 0.6844 (mp) cc_final: 0.6348 (mp) REVERT: D 18 ASP cc_start: 0.6963 (p0) cc_final: 0.6311 (p0) REVERT: D 90 PHE cc_start: 0.7378 (m-80) cc_final: 0.7092 (m-80) REVERT: D 108 ASP cc_start: 0.6122 (t70) cc_final: 0.5815 (t0) REVERT: J 108 MET cc_start: 0.6857 (mmm) cc_final: 0.6530 (mmm) REVERT: K 8 LEU cc_start: 0.6623 (mm) cc_final: 0.6237 (mm) REVERT: K 73 ASP cc_start: 0.6494 (p0) cc_final: 0.5771 (p0) REVERT: N 53 THR cc_start: 0.8673 (p) cc_final: 0.8443 (t) REVERT: N 54 LEU cc_start: 0.8181 (mt) cc_final: 0.7737 (mm) REVERT: N 107 ASN cc_start: 0.7582 (t0) cc_final: 0.7167 (t0) REVERT: P 5 LYS cc_start: 0.7374 (mttm) cc_final: 0.7074 (mttm) REVERT: P 111 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6751 (mm-30) REVERT: P 112 ARG cc_start: 0.6737 (ttm170) cc_final: 0.6080 (ttm-80) REVERT: Q 63 ARG cc_start: 0.5646 (mtt180) cc_final: 0.5424 (mtt180) REVERT: Q 89 ILE cc_start: 0.6926 (mm) cc_final: 0.6710 (mm) REVERT: Q 90 ASP cc_start: 0.6838 (p0) cc_final: 0.6573 (p0) REVERT: S 51 LEU cc_start: 0.7879 (pp) cc_final: 0.7583 (pp) REVERT: S 81 SER cc_start: 0.7764 (t) cc_final: 0.7458 (m) REVERT: 0 3 GLN cc_start: 0.6744 (mp-120) cc_final: 0.6149 (mt0) REVERT: 0 18 HIS cc_start: 0.7233 (m90) cc_final: 0.6890 (m90) REVERT: 0 53 VAL cc_start: 0.7154 (p) cc_final: 0.6678 (p) REVERT: Z 13 ILE cc_start: 0.5131 (mt) cc_final: 0.4578 (tt) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.6309 time to fit residues: 504.5908 Evaluate side-chains 393 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 371 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 chunk 370 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 67012 Z= 0.276 Angle : 0.657 9.876 100893 Z= 0.339 Chirality : 0.037 0.272 13005 Planarity : 0.005 0.088 4966 Dihedral : 24.051 169.403 34819 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.72 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.17), residues: 2076 helix: -1.22 (0.20), residues: 530 sheet: -1.00 (0.26), residues: 405 loop : -1.75 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 15 HIS 0.006 0.002 HIS N 16 PHE 0.018 0.002 PHE L 107 TYR 0.020 0.002 TYR S 38 ARG 0.017 0.001 ARG S 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 18 ASP cc_start: 0.7091 (p0) cc_final: 0.6603 (p0) REVERT: D 90 PHE cc_start: 0.7196 (m-80) cc_final: 0.6914 (m-80) REVERT: E 188 MET cc_start: 0.6134 (tpp) cc_final: 0.5858 (tpp) REVERT: J 14 ASP cc_start: 0.5966 (p0) cc_final: 0.5511 (p0) REVERT: J 108 MET cc_start: 0.6750 (mmm) cc_final: 0.6473 (mmm) REVERT: J 122 LEU cc_start: 0.8111 (tp) cc_final: 0.7865 (tt) REVERT: K 73 ASP cc_start: 0.6457 (p0) cc_final: 0.5883 (p0) REVERT: N 53 THR cc_start: 0.8701 (p) cc_final: 0.8319 (t) REVERT: N 54 LEU cc_start: 0.8150 (mt) cc_final: 0.7731 (mm) REVERT: N 107 ASN cc_start: 0.7615 (t0) cc_final: 0.7152 (t0) REVERT: N 118 ARG cc_start: 0.6583 (tmm160) cc_final: 0.6239 (tmm-80) REVERT: P 3 ILE cc_start: 0.7780 (pt) cc_final: 0.7478 (pt) REVERT: P 5 LYS cc_start: 0.7429 (mttm) cc_final: 0.7069 (mttm) REVERT: P 111 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6516 (mm-30) REVERT: P 112 ARG cc_start: 0.6931 (ttm170) cc_final: 0.6245 (ttm-80) REVERT: Q 63 ARG cc_start: 0.5826 (mtt180) cc_final: 0.5440 (mtt180) REVERT: Q 89 ILE cc_start: 0.6949 (mm) cc_final: 0.6627 (mm) REVERT: Q 90 ASP cc_start: 0.6646 (p0) cc_final: 0.6294 (p0) REVERT: S 22 ASP cc_start: 0.6379 (p0) cc_final: 0.6122 (p0) REVERT: S 24 ILE cc_start: 0.9016 (mm) cc_final: 0.8564 (mm) REVERT: S 51 LEU cc_start: 0.7710 (pp) cc_final: 0.7396 (pp) REVERT: S 81 SER cc_start: 0.7800 (t) cc_final: 0.7438 (m) REVERT: S 86 MET cc_start: 0.6119 (ppp) cc_final: 0.5452 (ppp) REVERT: Y 8 GLU cc_start: 0.6353 (tt0) cc_final: 0.5882 (tt0) REVERT: 0 3 GLN cc_start: 0.6400 (mp10) cc_final: 0.6023 (mt0) REVERT: 0 18 HIS cc_start: 0.7284 (m90) cc_final: 0.6675 (m-70) REVERT: Z 13 ILE cc_start: 0.4892 (mt) cc_final: 0.4273 (tt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.6347 time to fit residues: 511.7937 Evaluate side-chains 391 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 0.5980 chunk 393 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 412 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Q 71 ASN R 6 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN 2 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.8227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 67012 Z= 0.143 Angle : 0.563 10.915 100893 Z= 0.290 Chirality : 0.032 0.243 13005 Planarity : 0.005 0.055 4966 Dihedral : 23.801 172.933 34819 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2076 helix: -0.80 (0.22), residues: 522 sheet: -0.90 (0.26), residues: 411 loop : -1.49 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 15 HIS 0.003 0.001 HIS N 16 PHE 0.019 0.002 PHE S 75 TYR 0.018 0.001 TYR N 112 ARG 0.015 0.001 ARG D 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 GLU cc_start: 0.7949 (pp20) cc_final: 0.7594 (pp20) REVERT: J 108 MET cc_start: 0.6490 (mmm) cc_final: 0.6075 (mmm) REVERT: K 73 ASP cc_start: 0.6247 (p0) cc_final: 0.5664 (p0) REVERT: N 53 THR cc_start: 0.8519 (p) cc_final: 0.8087 (t) REVERT: N 54 LEU cc_start: 0.7949 (mt) cc_final: 0.7519 (mm) REVERT: P 5 LYS cc_start: 0.7443 (mttm) cc_final: 0.7093 (mttm) REVERT: P 111 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6484 (mm-30) REVERT: P 112 ARG cc_start: 0.6694 (ttm170) cc_final: 0.6057 (ttm-80) REVERT: Q 63 ARG cc_start: 0.5476 (mtt180) cc_final: 0.5228 (mtt180) REVERT: Q 90 ASP cc_start: 0.6406 (p0) cc_final: 0.6150 (p0) REVERT: S 33 LEU cc_start: 0.7319 (mm) cc_final: 0.7108 (mt) REVERT: S 81 SER cc_start: 0.7643 (t) cc_final: 0.7337 (m) REVERT: Y 28 LEU cc_start: 0.7610 (pp) cc_final: 0.7106 (pp) REVERT: Y 31 GLN cc_start: 0.5209 (pp30) cc_final: 0.4887 (pp30) REVERT: 0 3 GLN cc_start: 0.6335 (mp10) cc_final: 0.6111 (mt0) REVERT: 0 18 HIS cc_start: 0.7348 (m90) cc_final: 0.6604 (m-70) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.6360 time to fit residues: 547.4606 Evaluate side-chains 412 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 302 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 328 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 337 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN J 135 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN Q 80 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047680 restraints weight = 362603.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049407 restraints weight = 140267.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050422 restraints weight = 82558.182| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.8659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 67012 Z= 0.289 Angle : 0.679 11.388 100893 Z= 0.349 Chirality : 0.038 0.318 13005 Planarity : 0.006 0.084 4966 Dihedral : 24.011 167.410 34819 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2076 helix: -1.05 (0.21), residues: 533 sheet: -0.92 (0.25), residues: 435 loop : -1.64 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 15 HIS 0.009 0.002 HIS N 16 PHE 0.028 0.003 PHE D 68 TYR 0.019 0.002 TYR N 94 ARG 0.019 0.001 ARG D 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10355.78 seconds wall clock time: 183 minutes 11.67 seconds (10991.67 seconds total)