Starting phenix.real_space_refine on Mon Sep 23 13:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w77_21569/09_2024/6w77_21569.cif" } resolution = 3.6 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= 0.000 sd= 1.000 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 1519 5.49 5 S 54 5.16 5 C 24131 2.51 5 N 8951 2.21 5 O 13285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 47940 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 32594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32594 Classifications: {'RNA': 1519} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 84, 'rna3p_pur': 755, 'rna3p_pyr': 569} Link IDs: {'rna2p': 194, 'rna3p': 1324} Chain breaks: 3 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1016 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 858 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 20.06, per 1000 atoms: 0.42 Number of scatterers: 47940 At special positions: 0 Unit cell: (204.943, 221.038, 168.461, 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 54 16.00 P 1519 15.00 O 13285 8.00 N 8951 7.00 C 24131 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: 8.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 40.6% alpha, 18.3% beta 487 base pairs and 770 stacking pairs defined. Time for finding SS restraints: 17.11 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.627A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.879A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.857A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 128 through 139 removed outlier: 4.068A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.660A pdb=" N GLY C 144 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.018A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 removed outlier: 3.505A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 147 through 150 Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.962A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 removed outlier: 4.435A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.591A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.731A pdb=" N ILE E 164 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.878A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.986A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.666A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.922A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'I' and resid 33 through 38 Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.517A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL I 47 " --> pdb=" O ARG I 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 43 through 47' Processing helix chain 'I' and resid 48 through 54 removed outlier: 3.671A pdb=" N GLU I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.682A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 removed outlier: 3.884A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 29 removed outlier: 4.926A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 58 Processing helix chain 'K' and resid 59 through 72 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'L' and resid 3 through 9 Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 4.587A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 78 Processing helix chain 'M' and resid 84 through 91 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.665A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.759A pdb=" N ALA N 7 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG N 8 " --> pdb=" O SER N 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 31 removed outlier: 4.421A pdb=" N LEU N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 48 removed outlier: 3.537A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 39 Processing helix chain 'O' and resid 41 through 45 removed outlier: 4.100A pdb=" N GLU O 45 " --> pdb=" O HIS O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.659A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.521A pdb=" N TYR O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.635A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.077A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'S' and resid 11 through 24 Processing helix chain 'S' and resid 40 through 44 Processing helix chain 'S' and resid 69 through 74 Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.789A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 84 removed outlier: 3.713A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.802A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.554A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 182 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 12 through 17 removed outlier: 4.912A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.768A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 46 removed outlier: 7.803A pdb=" N HIS F 37 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N GLU F 65 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 39 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN F 63 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 24 through 28 removed outlier: 6.181A pdb=" N GLU H 58 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL H 51 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU H 60 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE H 49 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR H 62 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AB1, first strand: chain 'H' and resid 74 through 77 removed outlier: 6.951A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 5 through 7 removed outlier: 4.044A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 18.981A pdb=" N LYS I 26 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 14.205A pdb=" N VAL I 66 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'J' and resid 45 through 51 removed outlier: 3.653A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 41 through 44 removed outlier: 7.024A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP K 44 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL K 32 " --> pdb=" O TRP K 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE K 23 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K 84 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR K 111 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.800A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR L 95 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 50 through 51 removed outlier: 6.196A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 8 through 14 removed outlier: 8.484A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Q 11 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS Q 71 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS Q 45 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER Q 72 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR Q 74 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 30 through 32 removed outlier: 5.802A pdb=" N LEU S 30 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS S 51 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1224 hydrogen bonds 1964 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 770 stacking parallelities Total time for adding SS restraints: 42.15 Time building geometry restraints manager: 10.37 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: 7077 1.33 - 1.45: 21313 1.45 - 1.57: 20542 1.57 - 1.69: 3031 1.69 - 1.81: 95 Bond restraints: 52058 Sorted by residual: bond pdb=" O3' U A1078 " pdb=" P G A1079 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' U A1075 " pdb=" P U A1076 " ideal model delta sigma weight residual 1.607 1.564 0.043 1.50e-02 4.44e+03 8.11e+00 bond pdb=" O3' G A1079 " pdb=" P A A1080 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 6.17e+00 bond pdb=" C3' U A1083 " pdb=" O3' U A1083 " ideal model delta sigma weight residual 1.417 1.454 -0.037 1.50e-02 4.44e+03 5.95e+00 bond pdb=" O3' A A1082 " pdb=" P U A1083 " ideal model delta sigma weight residual 1.607 1.572 0.035 1.50e-02 4.44e+03 5.54e+00 ... (remaining 52053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 77640 3.50 - 6.99: 157 6.99 - 10.49: 12 10.49 - 13.98: 1 13.98 - 17.48: 2 Bond angle restraints: 77812 Sorted by residual: angle pdb=" O2' C A 924 " pdb=" C2' C A 924 " pdb=" C1' C A 924 " ideal model delta sigma weight residual 108.40 90.92 17.48 1.50e+00 4.44e-01 1.36e+02 angle pdb=" O3' C A 924 " pdb=" C3' C A 924 " pdb=" C2' C A 924 " ideal model delta sigma weight residual 113.70 96.51 17.19 1.50e+00 4.44e-01 1.31e+02 angle pdb=" C3' C A 924 " pdb=" C2' C A 924 " pdb=" O2' C A 924 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.50e+00 4.44e-01 6.29e+01 angle pdb=" O2' A A1082 " pdb=" C2' A A1082 " pdb=" C1' A A1082 " ideal model delta sigma weight residual 108.40 97.95 10.45 1.50e+00 4.44e-01 4.86e+01 angle pdb=" C3' U A1076 " pdb=" C2' U A1076 " pdb=" O2' U A1076 " ideal model delta sigma weight residual 110.70 101.75 8.95 1.50e+00 4.44e-01 3.56e+01 ... (remaining 77807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 29445 35.82 - 71.64: 3496 71.64 - 107.45: 429 107.45 - 143.27: 9 143.27 - 179.09: 12 Dihedral angle restraints: 33391 sinusoidal: 27810 harmonic: 5581 Sorted by residual: dihedral pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" C2' A A1431 " pdb=" C1' A A1431 " ideal model delta sinusoidal sigma weight residual -35.00 30.96 -65.96 1 8.00e+00 1.56e-02 8.89e+01 dihedral pdb=" O4' U A 439 " pdb=" C1' U A 439 " pdb=" N1 U A 439 " pdb=" C2 U A 439 " ideal model delta sinusoidal sigma weight residual 200.00 35.96 164.04 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" C5' A A1431 " pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" O3' A A1431 " ideal model delta sinusoidal sigma weight residual 147.00 84.17 62.83 1 8.00e+00 1.56e-02 8.15e+01 ... (remaining 33388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 9824 0.117 - 0.235: 100 0.235 - 0.352: 6 0.352 - 0.469: 2 0.469 - 0.587: 1 Chirality restraints: 9933 Sorted by residual: chirality pdb=" C3' U A1065 " pdb=" C4' U A1065 " pdb=" O3' U A1065 " pdb=" C2' U A1065 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.60e+00 chirality pdb=" C3' C A 924 " pdb=" C4' C A 924 " pdb=" O3' C A 924 " pdb=" C2' C A 924 " both_signs ideal model delta sigma weight residual False -2.48 -2.85 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C2' U A1073 " pdb=" C3' U A1073 " pdb=" O2' U A1073 " pdb=" C1' U A1073 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 9930 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1077 " -0.062 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" N9 G A1077 " 0.058 2.00e-02 2.50e+03 pdb=" C8 G A1077 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A1077 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1077 " -0.015 2.00e-02 2.50e+03 pdb=" O6 G A1077 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A1077 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N2 G A1077 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G A1077 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G A1077 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1083 " 0.031 2.00e-02 2.50e+03 1.49e-02 5.03e+00 pdb=" N1 U A1083 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U A1083 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U A1083 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U A1083 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U A1083 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U A1083 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A1083 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1082 " -0.027 2.00e-02 2.50e+03 1.32e-02 4.80e+00 pdb=" N9 A A1082 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A A1082 " 0.005 2.00e-02 2.50e+03 pdb=" N7 A A1082 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A A1082 " -0.008 2.00e-02 2.50e+03 pdb=" C6 A A1082 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A1082 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A A1082 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A A1082 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A1082 " 0.002 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1568 2.65 - 3.21: 39875 3.21 - 3.77: 92755 3.77 - 4.34: 120307 4.34 - 4.90: 162775 Nonbonded interactions: 417280 Sorted by model distance: nonbonded pdb=" OP1 C A 738 " pdb=" OH TYR F 4 " model vdw 2.084 3.040 nonbonded pdb=" O2' G A 925 " pdb=" O4' G A 926 " model vdw 2.147 3.040 nonbonded pdb=" O6 G A1419 " pdb=" O4 U A1481 " model vdw 2.158 2.432 nonbonded pdb=" O6 G A1064 " pdb=" N4 C A1192 " model vdw 2.171 3.120 nonbonded pdb=" OG SER D 192 " pdb=" OD1 ASP D 194 " model vdw 2.181 3.040 ... (remaining 417275 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.860 Check model and map are aligned: 0.280 Set scattering table: 0.340 Process input model: 114.940 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 52058 Z= 0.133 Angle : 0.530 17.481 77812 Z= 0.301 Chirality : 0.033 0.587 9933 Planarity : 0.003 0.040 4217 Dihedral : 23.069 179.089 29787 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 4.53 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.17), residues: 1913 helix: -1.41 (0.17), residues: 666 sheet: -1.79 (0.24), residues: 346 loop : -2.85 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.006 0.001 HIS T 75 PHE 0.018 0.001 PHE N 20 TYR 0.008 0.001 TYR O 78 ARG 0.007 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 575 time to evaluate : 1.992 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: C 40 GLN cc_start: 0.7369 (tt0) cc_final: 0.7165 (tm-30) REVERT: C 41 TYR cc_start: 0.6724 (t80) cc_final: 0.5591 (t80) REVERT: C 167 TYR cc_start: 0.5368 (m-80) cc_final: 0.5143 (m-80) REVERT: D 116 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7373 (tm-30) REVERT: E 26 LYS cc_start: 0.8503 (ptmm) cc_final: 0.8073 (pttm) REVERT: E 116 GLU cc_start: 0.7209 (pp20) cc_final: 0.6434 (tp30) REVERT: H 94 LYS cc_start: 0.7841 (ttmm) cc_final: 0.6904 (tppt) REVERT: J 24 GLU cc_start: 0.4683 (pt0) cc_final: 0.4428 (pt0) REVERT: K 93 ARG cc_start: 0.5066 (mpt180) cc_final: 0.4748 (ttp80) REVERT: K 125 LYS cc_start: 0.6547 (mtpt) cc_final: 0.6110 (mmtt) REVERT: L 11 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.8004 (Cg_exo) REVERT: O 36 ILE cc_start: 0.7763 (mt) cc_final: 0.7535 (mt) REVERT: O 63 ARG cc_start: 0.6320 (ttp-170) cc_final: 0.6001 (ttp80) REVERT: Q 70 THR cc_start: 0.7808 (m) cc_final: 0.7545 (p) REVERT: S 80 ARG cc_start: 0.4736 (mmp80) cc_final: 0.4029 (mmm160) REVERT: T 23 SER cc_start: 0.9003 (t) cc_final: 0.8632 (m) REVERT: T 57 ILE cc_start: 0.8368 (tt) cc_final: 0.7450 (mp) REVERT: T 78 ASN cc_start: 0.7857 (m-40) cc_final: 0.7543 (m110) outliers start: 2 outliers final: 0 residues processed: 575 average time/residue: 0.5909 time to fit residues: 520.5334 Evaluate side-chains 394 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 172 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN C 101 ASN C 175 HIS D 59 GLN D 74 ASN D 100 ASN D 120 HIS D 131 ASN D 136 GLN D 164 GLN E 70 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 49 GLN J 70 HIS K 15 GLN K 119 ASN L 5 ASN M 7 ASN M 13 HIS P 59 HIS R 31 ASN T 21 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52058 Z= 0.205 Angle : 0.628 12.962 77812 Z= 0.316 Chirality : 0.034 0.207 9933 Planarity : 0.005 0.088 4217 Dihedral : 23.472 171.119 25905 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.11 % Favored : 92.79 % Rotamer: Outliers : 3.72 % Allowed : 16.44 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -2.38 (0.18), residues: 1913 helix: -0.57 (0.19), residues: 697 sheet: -1.27 (0.26), residues: 344 loop : -2.57 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 42 HIS 0.005 0.001 HIS O 50 PHE 0.014 0.002 PHE I 19 TYR 0.024 0.002 TYR C 192 ARG 0.011 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 437 time to evaluate : 2.003 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: C 22 PHE cc_start: 0.6861 (t80) cc_final: 0.6319 (t80) REVERT: C 28 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: C 40 GLN cc_start: 0.7713 (tt0) cc_final: 0.7470 (tm-30) REVERT: C 41 TYR cc_start: 0.6691 (t80) cc_final: 0.5589 (t80) REVERT: E 26 LYS cc_start: 0.8606 (ptmm) cc_final: 0.8139 (pttm) REVERT: F 4 TYR cc_start: 0.6406 (m-80) cc_final: 0.5788 (m-80) REVERT: F 42 TRP cc_start: 0.5408 (m-10) cc_final: 0.4959 (m100) REVERT: L 11 PRO cc_start: 0.8222 (Cg_endo) cc_final: 0.7985 (Cg_exo) REVERT: M 71 GLU cc_start: 0.7044 (pp20) cc_final: 0.6826 (pt0) REVERT: N 15 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.5148 (pp) REVERT: O 36 ILE cc_start: 0.7795 (mt) cc_final: 0.7591 (mt) REVERT: O 78 TYR cc_start: 0.6770 (t80) cc_final: 0.6412 (t80) REVERT: P 1 MET cc_start: 0.7066 (pmm) cc_final: 0.6461 (pmm) REVERT: P 77 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6512 (tp30) REVERT: Q 30 LYS cc_start: 0.8239 (tttp) cc_final: 0.8013 (tttm) REVERT: Q 37 PHE cc_start: 0.7535 (m-10) cc_final: 0.7267 (m-10) REVERT: Q 68 SER cc_start: 0.8565 (p) cc_final: 0.8330 (t) REVERT: S 80 ARG cc_start: 0.5078 (mmp80) cc_final: 0.4103 (mmm160) REVERT: T 23 SER cc_start: 0.9060 (t) cc_final: 0.8668 (m) REVERT: T 61 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7938 (mm-40) REVERT: T 78 ASN cc_start: 0.7807 (m-40) cc_final: 0.7440 (m110) outliers start: 60 outliers final: 35 residues processed: 471 average time/residue: 0.5773 time to fit residues: 424.1883 Evaluate side-chains 406 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 369 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 304 optimal weight: 0.0020 chunk 104 optimal weight: 9.9990 chunk 245 optimal weight: 0.4980 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN D 40 GLN D 74 ASN D 131 ASN D 164 GLN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 52058 Z= 0.149 Angle : 0.542 9.672 77812 Z= 0.275 Chirality : 0.032 0.207 9933 Planarity : 0.004 0.043 4217 Dihedral : 23.391 171.913 25905 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.36 % Rotamer: Outliers : 3.78 % Allowed : 18.67 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -1.97 (0.18), residues: 1913 helix: -0.20 (0.19), residues: 704 sheet: -0.95 (0.27), residues: 340 loop : -2.41 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.005 0.001 HIS F 58 PHE 0.018 0.001 PHE S 40 TYR 0.014 0.001 TYR C 192 ARG 0.009 0.001 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 402 time to evaluate : 2.021 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: C 28 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5875 (m-80) REVERT: C 40 GLN cc_start: 0.7764 (tt0) cc_final: 0.7441 (tm-30) REVERT: C 41 TYR cc_start: 0.6738 (t80) cc_final: 0.5629 (t80) REVERT: C 122 GLN cc_start: 0.6420 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: D 116 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 26 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8116 (pttm) REVERT: F 88 MET cc_start: 0.6968 (tpp) cc_final: 0.6713 (tpp) REVERT: I 61 ASP cc_start: 0.5521 (t0) cc_final: 0.5313 (t0) REVERT: J 97 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5747 (m-30) REVERT: L 9 ARG cc_start: 0.7344 (mtm110) cc_final: 0.7129 (mtm180) REVERT: L 11 PRO cc_start: 0.8264 (Cg_endo) cc_final: 0.8039 (Cg_exo) REVERT: O 71 LYS cc_start: 0.8002 (tttt) cc_final: 0.7782 (tttt) REVERT: O 78 TYR cc_start: 0.6876 (t80) cc_final: 0.6393 (t80) REVERT: O 81 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7981 (mp) REVERT: P 1 MET cc_start: 0.7012 (pmm) cc_final: 0.6445 (pmm) REVERT: Q 30 LYS cc_start: 0.8306 (tttp) cc_final: 0.8071 (tttm) REVERT: Q 37 PHE cc_start: 0.7584 (m-10) cc_final: 0.7335 (m-10) REVERT: Q 75 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7579 (tt) REVERT: R 33 ILE cc_start: 0.6979 (pt) cc_final: 0.6590 (tt) REVERT: S 80 ARG cc_start: 0.5267 (mmp80) cc_final: 0.4198 (mmm160) REVERT: T 23 SER cc_start: 0.9073 (t) cc_final: 0.8644 (m) REVERT: T 57 ILE cc_start: 0.8427 (tt) cc_final: 0.7959 (mp) REVERT: T 78 ASN cc_start: 0.7674 (m-40) cc_final: 0.7410 (m110) outliers start: 61 outliers final: 36 residues processed: 435 average time/residue: 0.6213 time to fit residues: 432.0397 Evaluate side-chains 416 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 375 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 325 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 ASN D 164 GLN F 52 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN H 21 ASN I 36 GLN I 80 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 52058 Z= 0.267 Angle : 0.715 10.158 77812 Z= 0.362 Chirality : 0.039 0.249 9933 Planarity : 0.006 0.049 4217 Dihedral : 23.567 169.578 25905 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.94 % Favored : 90.96 % Rotamer: Outliers : 4.84 % Allowed : 22.02 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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 (0.18), residues: 1913 helix: -0.49 (0.18), residues: 704 sheet: -1.02 (0.27), residues: 341 loop : -2.58 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 42 HIS 0.005 0.002 HIS D 41 PHE 0.014 0.002 PHE P 16 TYR 0.029 0.002 TYR C 192 ARG 0.009 0.001 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 405 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 PHE cc_start: 0.7525 (t80) cc_final: 0.7239 (t80) REVERT: C 28 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6195 (m-80) REVERT: C 41 TYR cc_start: 0.6640 (t80) cc_final: 0.5931 (t80) REVERT: C 42 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6678 (mp) REVERT: C 125 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5920 (mpp80) REVERT: D 58 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8743 (tttm) REVERT: D 116 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: E 26 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8120 (pttm) REVERT: F 88 MET cc_start: 0.6849 (tpp) cc_final: 0.6535 (tpp) REVERT: I 61 ASP cc_start: 0.5224 (t0) cc_final: 0.4876 (t0) REVERT: I 84 ARG cc_start: 0.6382 (ttt180) cc_final: 0.6131 (ttt180) REVERT: K 93 ARG cc_start: 0.5999 (mpt180) cc_final: 0.5220 (ttp80) REVERT: N 9 GLU cc_start: 0.4804 (OUTLIER) cc_final: 0.3339 (tp30) REVERT: Q 37 PHE cc_start: 0.7660 (m-10) cc_final: 0.7459 (m-10) REVERT: R 33 ILE cc_start: 0.7039 (pt) cc_final: 0.6570 (tt) REVERT: R 48 ARG cc_start: 0.5733 (mpt-90) cc_final: 0.5518 (mtt-85) REVERT: S 27 LYS cc_start: 0.6834 (ptmt) cc_final: 0.6456 (pttm) REVERT: S 80 ARG cc_start: 0.5418 (mmp80) cc_final: 0.4458 (mmm160) REVERT: T 23 SER cc_start: 0.8989 (t) cc_final: 0.8568 (m) REVERT: T 78 ASN cc_start: 0.7796 (m-40) cc_final: 0.7524 (m110) outliers start: 78 outliers final: 54 residues processed: 457 average time/residue: 0.5614 time to fit residues: 400.3082 Evaluate side-chains 433 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 374 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 3 HIS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 80 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 0.9990 chunk 184 optimal weight: 0.0980 chunk 4 optimal weight: 10.0000 chunk 242 optimal weight: 0.1980 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 225 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS D 74 ASN D 164 GLN E 146 ASN F 37 HIS ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN H 16 ASN J 70 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 70 HIS ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 52058 Z= 0.131 Angle : 0.554 10.247 77812 Z= 0.282 Chirality : 0.032 0.291 9933 Planarity : 0.004 0.045 4217 Dihedral : 23.362 172.890 25905 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 3.29 % Allowed : 24.38 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -1.76 (0.18), residues: 1913 helix: 0.06 (0.19), residues: 708 sheet: -0.91 (0.27), residues: 336 loop : -2.34 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 200 HIS 0.004 0.001 HIS P 59 PHE 0.016 0.001 PHE S 40 TYR 0.020 0.001 TYR I 89 ARG 0.006 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 409 time to evaluate : 1.988 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: C 28 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: C 40 GLN cc_start: 0.7993 (tt0) cc_final: 0.7258 (tm-30) REVERT: C 41 TYR cc_start: 0.6551 (t80) cc_final: 0.5548 (t80) REVERT: C 122 GLN cc_start: 0.7085 (tp-100) cc_final: 0.6857 (tp40) REVERT: D 58 LYS cc_start: 0.8936 (tmtt) cc_final: 0.8707 (tttm) REVERT: D 116 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7768 (tm-30) REVERT: E 26 LYS cc_start: 0.8484 (ptmm) cc_final: 0.7995 (pttm) REVERT: E 54 ARG cc_start: 0.7969 (tpp80) cc_final: 0.7689 (tpp80) REVERT: E 121 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.5221 (m90) REVERT: F 54 LEU cc_start: 0.7551 (tp) cc_final: 0.7224 (mt) REVERT: F 88 MET cc_start: 0.6627 (tpp) cc_final: 0.6330 (tpp) REVERT: H 52 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6519 (mm-30) REVERT: N 6 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5394 (mtpt) REVERT: P 1 MET cc_start: 0.6967 (pmm) cc_final: 0.6704 (pmm) REVERT: P 77 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6363 (tp30) REVERT: Q 37 PHE cc_start: 0.7600 (m-10) cc_final: 0.7329 (m-10) REVERT: Q 75 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7573 (tt) REVERT: R 33 ILE cc_start: 0.6858 (pt) cc_final: 0.6468 (tt) REVERT: R 73 ARG cc_start: 0.5110 (OUTLIER) cc_final: 0.4249 (mtm110) REVERT: S 80 ARG cc_start: 0.5505 (mmp80) cc_final: 0.4471 (mmm160) REVERT: T 23 SER cc_start: 0.9046 (t) cc_final: 0.8589 (m) REVERT: T 78 ASN cc_start: 0.7642 (m-40) cc_final: 0.7253 (m110) outliers start: 53 outliers final: 31 residues processed: 444 average time/residue: 0.5791 time to fit residues: 399.7557 Evaluate side-chains 404 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 368 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 10.0000 chunk 293 optimal weight: 0.0000 chunk 64 optimal weight: 10.0000 chunk 191 optimal weight: 0.3980 chunk 80 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 overall best weight: 3.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 131 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN J 64 GLN J 70 HIS J 99 GLN K 109 ASN M 104 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 52058 Z= 0.271 Angle : 0.719 9.579 77812 Z= 0.360 Chirality : 0.039 0.259 9933 Planarity : 0.005 0.058 4217 Dihedral : 23.511 169.653 25905 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.62 % Favored : 90.28 % Rotamer: Outliers : 5.21 % Allowed : 24.01 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -2.00 (0.18), residues: 1913 helix: -0.19 (0.19), residues: 702 sheet: -0.88 (0.27), residues: 341 loop : -2.50 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 200 HIS 0.005 0.002 HIS O 46 PHE 0.030 0.002 PHE S 40 TYR 0.027 0.002 TYR R 23 ARG 0.016 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 393 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: C 41 TYR cc_start: 0.6594 (t80) cc_final: 0.5946 (t80) REVERT: D 116 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: E 26 LYS cc_start: 0.8574 (ptmm) cc_final: 0.8077 (pttm) REVERT: F 4 TYR cc_start: 0.6998 (m-80) cc_final: 0.6549 (m-80) REVERT: F 88 MET cc_start: 0.7099 (tpp) cc_final: 0.6626 (tpp) REVERT: I 112 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6556 (ptm160) REVERT: K 69 ARG cc_start: 0.4904 (ptp90) cc_final: 0.4534 (ptm-80) REVERT: M 68 LEU cc_start: 0.4376 (pt) cc_final: 0.3771 (tp) REVERT: M 99 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.5432 (mp10) REVERT: Q 37 PHE cc_start: 0.7733 (m-10) cc_final: 0.7489 (m-10) REVERT: Q 75 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7603 (tt) REVERT: Q 80 GLU cc_start: 0.7989 (mp0) cc_final: 0.7779 (mp0) REVERT: R 33 ILE cc_start: 0.7049 (pt) cc_final: 0.6638 (tt) REVERT: R 73 ARG cc_start: 0.5318 (OUTLIER) cc_final: 0.4129 (mtm110) REVERT: S 80 ARG cc_start: 0.5359 (mmp80) cc_final: 0.4473 (mmm160) REVERT: T 23 SER cc_start: 0.8962 (t) cc_final: 0.8553 (m) REVERT: T 78 ASN cc_start: 0.7775 (m-40) cc_final: 0.7510 (m110) outliers start: 84 outliers final: 57 residues processed: 449 average time/residue: 0.5736 time to fit residues: 404.9627 Evaluate side-chains 429 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 367 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 152 MET Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 chunk 182 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 198 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 ASN C 122 GLN D 40 GLN D 41 HIS D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN I 36 GLN J 64 GLN J 99 GLN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN T 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 52058 Z= 0.169 Angle : 0.603 10.448 77812 Z= 0.305 Chirality : 0.034 0.221 9933 Planarity : 0.005 0.065 4217 Dihedral : 23.409 171.497 25905 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.48 % Favored : 92.47 % Rotamer: Outliers : 4.28 % Allowed : 25.06 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -1.82 (0.18), residues: 1913 helix: -0.01 (0.19), residues: 702 sheet: -0.81 (0.27), residues: 340 loop : -2.41 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 200 HIS 0.009 0.001 HIS D 41 PHE 0.013 0.001 PHE C 22 TYR 0.023 0.001 TYR I 89 ARG 0.010 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 388 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: C 40 GLN cc_start: 0.8343 (tt0) cc_final: 0.7542 (tm-30) REVERT: C 201 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6838 (mp) REVERT: D 116 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: E 26 LYS cc_start: 0.8535 (ptmm) cc_final: 0.8052 (pttm) REVERT: E 121 HIS cc_start: 0.6764 (OUTLIER) cc_final: 0.5195 (m90) REVERT: F 4 TYR cc_start: 0.6765 (m-80) cc_final: 0.6360 (m-80) REVERT: F 54 LEU cc_start: 0.8299 (mt) cc_final: 0.7172 (tp) REVERT: F 88 MET cc_start: 0.6631 (tpp) cc_final: 0.6229 (tpp) REVERT: H 3 MET cc_start: 0.5706 (tpt) cc_final: 0.5382 (pmm) REVERT: I 112 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.6766 (ptm160) REVERT: K 69 ARG cc_start: 0.4940 (ptp90) cc_final: 0.4654 (ptm-80) REVERT: N 73 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7393 (tp) REVERT: Q 75 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7613 (tt) REVERT: Q 80 GLU cc_start: 0.7879 (mp0) cc_final: 0.7631 (mp0) REVERT: R 33 ILE cc_start: 0.7046 (pt) cc_final: 0.6637 (tt) REVERT: S 80 ARG cc_start: 0.5395 (mmp80) cc_final: 0.4489 (mmm160) REVERT: T 23 SER cc_start: 0.8965 (t) cc_final: 0.8494 (m) REVERT: T 78 ASN cc_start: 0.7703 (m-40) cc_final: 0.7435 (m110) outliers start: 69 outliers final: 54 residues processed: 433 average time/residue: 0.5813 time to fit residues: 396.5850 Evaluate side-chains 429 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 369 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain S residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 221 optimal weight: 0.5980 chunk 160 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 0.5980 overall best weight: 2.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 GLN D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 64 GLN J 99 GLN K 109 ASN M 104 ASN T 61 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 52058 Z= 0.182 Angle : 0.611 9.822 77812 Z= 0.308 Chirality : 0.035 0.241 9933 Planarity : 0.005 0.071 4217 Dihedral : 23.407 170.839 25905 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.68 % Favored : 91.27 % Rotamer: Outliers : 4.78 % Allowed : 25.50 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -1.77 (0.18), residues: 1913 helix: 0.04 (0.19), residues: 709 sheet: -0.85 (0.27), residues: 342 loop : -2.39 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 200 HIS 0.004 0.001 HIS O 46 PHE 0.026 0.002 PHE S 40 TYR 0.024 0.002 TYR I 89 ARG 0.011 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 383 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: C 40 GLN cc_start: 0.8345 (tt0) cc_final: 0.7495 (tm-30) REVERT: C 41 TYR cc_start: 0.6592 (t80) cc_final: 0.6138 (t80) REVERT: C 201 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6770 (mp) REVERT: D 116 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: E 26 LYS cc_start: 0.8510 (ptmm) cc_final: 0.8024 (pttm) REVERT: E 121 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.5263 (m90) REVERT: F 4 TYR cc_start: 0.6764 (m-80) cc_final: 0.6323 (m-80) REVERT: F 54 LEU cc_start: 0.8385 (mt) cc_final: 0.7257 (tp) REVERT: F 88 MET cc_start: 0.6671 (tpp) cc_final: 0.6141 (tpp) REVERT: H 3 MET cc_start: 0.5840 (tpt) cc_final: 0.5592 (pmm) REVERT: H 76 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: I 102 PHE cc_start: 0.6635 (m-10) cc_final: 0.6337 (m-80) REVERT: I 112 ARG cc_start: 0.7259 (ptm-80) cc_final: 0.6767 (ptm160) REVERT: K 69 ARG cc_start: 0.4951 (ptp90) cc_final: 0.4650 (ptm-80) REVERT: M 99 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.5487 (mp10) REVERT: N 73 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7364 (tp) REVERT: N 82 LYS cc_start: 0.6362 (mmmt) cc_final: 0.6008 (mmmt) REVERT: Q 75 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7613 (tt) REVERT: R 33 ILE cc_start: 0.7052 (pt) cc_final: 0.6604 (tt) REVERT: R 48 ARG cc_start: 0.5917 (mtt-85) cc_final: 0.5642 (mtt-85) REVERT: S 28 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5448 (pptt) REVERT: S 80 ARG cc_start: 0.5283 (mmp80) cc_final: 0.4418 (mmm160) REVERT: T 23 SER cc_start: 0.8943 (t) cc_final: 0.8454 (m) REVERT: T 78 ASN cc_start: 0.7746 (m-40) cc_final: 0.7507 (m110) outliers start: 77 outliers final: 55 residues processed: 432 average time/residue: 0.5952 time to fit residues: 408.2727 Evaluate side-chains 434 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 370 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 0.7980 chunk 311 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 237 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 301 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN I 3 ASN J 64 GLN M 104 ASN T 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 52058 Z= 0.135 Angle : 0.561 10.830 77812 Z= 0.284 Chirality : 0.032 0.253 9933 Planarity : 0.004 0.064 4217 Dihedral : 23.336 171.735 25905 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 4.22 % Allowed : 25.99 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -1.57 (0.19), residues: 1913 helix: 0.22 (0.19), residues: 711 sheet: -0.80 (0.28), residues: 342 loop : -2.26 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 200 HIS 0.004 0.001 HIS P 59 PHE 0.038 0.001 PHE M 62 TYR 0.023 0.001 TYR I 89 ARG 0.015 0.001 ARG C 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 389 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: C 40 GLN cc_start: 0.8232 (tt0) cc_final: 0.7452 (tm-30) REVERT: C 41 TYR cc_start: 0.6571 (t80) cc_final: 0.6140 (t80) REVERT: C 201 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6647 (mp) REVERT: D 104 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7245 (mpt180) REVERT: D 116 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: E 26 LYS cc_start: 0.8446 (ptmm) cc_final: 0.7965 (pttm) REVERT: F 4 TYR cc_start: 0.6686 (m-80) cc_final: 0.6270 (m-80) REVERT: F 45 ARG cc_start: 0.7545 (tpp-160) cc_final: 0.6832 (mmp-170) REVERT: F 54 LEU cc_start: 0.8399 (mt) cc_final: 0.7286 (tp) REVERT: F 88 MET cc_start: 0.6905 (tpp) cc_final: 0.6570 (tpp) REVERT: H 3 MET cc_start: 0.5799 (tpt) cc_final: 0.5518 (pmm) REVERT: H 76 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: I 102 PHE cc_start: 0.6591 (m-10) cc_final: 0.6321 (m-80) REVERT: I 112 ARG cc_start: 0.7309 (ptm-80) cc_final: 0.6779 (ptm160) REVERT: K 69 ARG cc_start: 0.4800 (ptp90) cc_final: 0.4516 (ptm-80) REVERT: N 82 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6004 (mmmt) REVERT: Q 75 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7593 (tt) REVERT: R 33 ILE cc_start: 0.6965 (pt) cc_final: 0.6577 (tt) REVERT: R 73 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4772 (mtm110) REVERT: S 28 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.4981 (pptt) REVERT: S 80 ARG cc_start: 0.5302 (mmp80) cc_final: 0.4441 (mmm160) REVERT: T 23 SER cc_start: 0.8998 (t) cc_final: 0.8494 (m) REVERT: T 78 ASN cc_start: 0.7633 (m-40) cc_final: 0.7336 (m110) outliers start: 68 outliers final: 53 residues processed: 433 average time/residue: 0.5611 time to fit residues: 380.2305 Evaluate side-chains 431 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 371 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 HIS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 3.9990 chunk 320 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 335 optimal weight: 8.9990 chunk 309 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN J 64 GLN M 104 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 52058 Z= 0.262 Angle : 0.726 13.051 77812 Z= 0.363 Chirality : 0.039 0.338 9933 Planarity : 0.006 0.093 4217 Dihedral : 23.511 169.449 25905 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.14 % Favored : 89.81 % Rotamer: Outliers : 4.65 % Allowed : 26.61 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % 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: -2.00 (0.18), residues: 1913 helix: -0.21 (0.19), residues: 707 sheet: -0.85 (0.28), residues: 336 loop : -2.50 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 166 HIS 0.007 0.001 HIS F 55 PHE 0.034 0.003 PHE M 62 TYR 0.027 0.002 TYR C 192 ARG 0.016 0.001 ARG M 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 380 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 28 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: D 116 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: E 26 LYS cc_start: 0.8561 (ptmm) cc_final: 0.8128 (pttm) REVERT: E 121 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.5339 (m90) REVERT: F 4 TYR cc_start: 0.6890 (m-80) cc_final: 0.6491 (m-80) REVERT: F 45 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.7158 (mmp-170) REVERT: H 76 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: I 102 PHE cc_start: 0.6739 (m-10) cc_final: 0.6393 (m-80) REVERT: I 112 ARG cc_start: 0.7368 (ptm-80) cc_final: 0.6896 (ptm-80) REVERT: K 69 ARG cc_start: 0.5040 (ptp90) cc_final: 0.4693 (ptm-80) REVERT: M 99 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5606 (mp10) REVERT: N 73 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7459 (tp) REVERT: P 76 LYS cc_start: 0.7067 (mmmt) cc_final: 0.6802 (mmmt) REVERT: Q 75 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7613 (tt) REVERT: R 33 ILE cc_start: 0.7087 (pt) cc_final: 0.6633 (tt) REVERT: R 73 ARG cc_start: 0.5414 (OUTLIER) cc_final: 0.4742 (mtm110) REVERT: S 28 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5511 (pptt) REVERT: S 80 ARG cc_start: 0.5337 (mmp80) cc_final: 0.4484 (mmm160) REVERT: T 23 SER cc_start: 0.8961 (t) cc_final: 0.8457 (m) REVERT: T 78 ASN cc_start: 0.7823 (m-40) cc_final: 0.7591 (m110) outliers start: 75 outliers final: 59 residues processed: 435 average time/residue: 0.5723 time to fit residues: 390.1267 Evaluate side-chains 427 residues out of total 1613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 359 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 121 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 3 LEU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 73 ARG Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN E 73 ASN E 146 ASN ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN J 64 GLN M 51 GLN M 104 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133749 restraints weight = 143113.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.135264 restraints weight = 59308.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136184 restraints weight = 31269.335| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 52058 Z= 0.408 Angle : 0.934 13.506 77812 Z= 0.464 Chirality : 0.048 0.331 9933 Planarity : 0.007 0.104 4217 Dihedral : 24.057 171.683 25905 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.81 % Favored : 88.13 % Rotamer: Outliers : 4.90 % Allowed : 26.80 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.72 (0.17), residues: 1913 helix: -0.85 (0.18), residues: 687 sheet: -1.23 (0.27), residues: 330 loop : -2.85 (0.18), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP N 100 HIS 0.006 0.002 HIS O 46 PHE 0.036 0.003 PHE M 62 TYR 0.041 0.003 TYR C 192 ARG 0.016 0.001 ARG C 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7860.89 seconds wall clock time: 138 minutes 21.18 seconds (8301.18 seconds total)