Starting phenix.real_space_refine on Thu Oct 29 20:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.map" model { file = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afl_11769/10_2026/7afl_11769.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 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: 6 Type Number sf(0) Gaussians P 1054 5.49 5 Mg 25 5.21 5 S 50 5.16 5 C 17386 2.51 5 N 6369 2.21 5 O 9438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.26s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34322 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 22654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 22654 Classifications: {'RNA': 4, 'RNAv2': 1050} Modifications used: {'rna2p_pur': 77, 'rna2p_pyr': 54, 'rna3p': 5, 'rna3p_pur': 530, 'rna3p_pyr': 388} Link IDs: {'rna2p': 131, 'rna3p': 922} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 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: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} 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: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 6.65, per 1000 atoms: 0.19 Number of scatterers: 34322 At special positions: 0 Unit cell: (145.39, 211.575, 139.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 1054 15.00 Mg 25 11.99 O 9438 8.00 N 6369 7.00 C 17386 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 898.4 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 18 sheets defined 41.4% alpha, 19.9% beta 308 base pairs and 526 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.151A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.977A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 65 removed outlier: 3.563A pdb=" N TYR D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 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 120 removed outlier: 3.727A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.099A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 159 removed outlier: 4.037A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.753A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 108 through 118 removed outlier: 3.661A pdb=" N ALA E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 143 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 17 through 32 removed outlier: 3.734A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.977A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.583A pdb=" N ALA F 105 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 removed outlier: 3.709A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 95 through 100 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 59 through 66 Processing helix chain 'K' and resid 66 through 78 removed outlier: 3.883A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.628A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 118 removed outlier: 4.047A pdb=" N GLY L 118 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 removed outlier: 3.543A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 46 removed outlier: 3.669A pdb=" N LEU O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 72 removed outlier: 3.872A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 62 " --> pdb=" O ARG O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.885A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 12 through 17 Processing helix chain 'R' and resid 25 through 32 Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.665A pdb=" N LYS T 9 " --> pdb=" O LYS T 5 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 3.820A 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 removed outlier: 3.513A pdb=" N ASP T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 87 Processing helix chain 'V' and resid 7 through 26 removed outlier: 4.707A pdb=" N GLN V 13 " --> pdb=" O GLN V 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS V 17 " --> pdb=" O GLN V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 47 Processing helix chain 'V' and resid 61 through 75 removed outlier: 3.654A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 85 Processing helix chain 'X' and resid 4 through 20 removed outlier: 4.130A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 47 through 66 removed outlier: 4.234A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU X 65 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'D' and resid 123 through 125 Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 24 removed outlier: 6.388A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER E 22 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE E 30 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 37 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.529A pdb=" N ALA E 125 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 35 through 45 removed outlier: 5.547A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 35 through 45 removed outlier: 5.547A pdb=" N ILE F 36 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU F 65 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 44 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA F 57 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA7, first strand: chain 'H' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AA9, first strand: chain 'H' and resid 110 through 112 removed outlier: 5.677A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 20 through 25 removed outlier: 4.348A pdb=" N VAL K 20 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE K 31 " --> pdb=" O HIS K 24 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 86 removed outlier: 3.704A pdb=" N VAL K 84 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 62 through 66 removed outlier: 3.512A pdb=" N VAL L 52 " --> pdb=" O TYR L 38 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG L 56 " --> pdb=" O CYS L 34 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N CYS L 34 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE L 82 " --> pdb=" O LYS L 30 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'P' and resid 3 through 5 removed outlier: 6.730A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 7 through 14 removed outlier: 16.048A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 12.585A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 16.588A pdb=" N LYS Q 71 " --> pdb=" O THR Q 41 " (cutoff:3.500A) removed outlier: 14.152A pdb=" N LYS Q 43 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N TRP Q 73 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N HIS Q 45 " --> pdb=" O TRP Q 73 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N HIS Q 47 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ARG Q 77 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP Q 73 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ARG Q 65 " --> pdb=" O TRP Q 73 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU Q 75 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLU Q 63 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG Q 77 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE Q 61 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'V' and resid 37 through 41 removed outlier: 5.217A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 22 through 29 removed outlier: 5.156A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU X 36 " --> pdb=" O GLU X 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER X 77 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE X 38 " --> pdb=" O SER X 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 132 through 136 removed outlier: 6.894A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 695 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 308 basepair parallelities 526 stacking parallelities Total time for adding SS restraints: 13.81 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5139 1.33 - 1.45: 15363 1.45 - 1.57: 14482 1.57 - 1.70: 2103 1.70 - 1.82: 88 Bond restraints: 37175 Sorted by residual: bond pdb=" O3' U A 571 " pdb=" P A A 572 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.20e-02 6.94e+03 1.32e+02 bond pdb=" N LYS H 56 " pdb=" CA LYS H 56 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.40e-03 1.83e+04 2.27e+01 bond pdb=" N VAL X 147 " pdb=" CA VAL X 147 " ideal model delta sigma weight residual 1.456 1.495 -0.039 8.70e-03 1.32e+04 1.98e+01 bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.464 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" N VAL V 92 " pdb=" CA VAL V 92 " ideal model delta sigma weight residual 1.460 1.490 -0.029 7.30e-03 1.88e+04 1.62e+01 ... (remaining 37170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 51998 2.65 - 5.29: 3282 5.29 - 7.94: 120 7.94 - 10.59: 23 10.59 - 13.23: 2 Bond angle restraints: 55425 Sorted by residual: angle pdb=" C ILE V 91 " pdb=" N VAL V 92 " pdb=" CA VAL V 92 " ideal model delta sigma weight residual 122.60 117.89 4.71 6.80e-01 2.16e+00 4.80e+01 angle pdb=" C LYS H 56 " pdb=" CA LYS H 56 " pdb=" CB LYS H 56 " ideal model delta sigma weight residual 111.00 116.99 -5.99 8.70e-01 1.32e+00 4.74e+01 angle pdb=" CA PRO V 30 " pdb=" N PRO V 30 " pdb=" CD PRO V 30 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" N PRO H 28 " pdb=" CA PRO H 28 " pdb=" C PRO H 28 " ideal model delta sigma weight residual 111.03 102.01 9.02 1.54e+00 4.22e-01 3.43e+01 angle pdb=" CA GLY K 43 " pdb=" C GLY K 43 " pdb=" O GLY K 43 " ideal model delta sigma weight residual 122.29 117.58 4.71 8.10e-01 1.52e+00 3.38e+01 ... (remaining 55420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 15834 20.59 - 41.19: 2197 41.19 - 61.78: 1681 61.78 - 82.37: 256 82.37 - 102.97: 7 Dihedral angle restraints: 19975 sinusoidal: 15705 harmonic: 4270 Sorted by residual: dihedral pdb=" C4' C A 90 " pdb=" C3' C A 90 " pdb=" C2' C A 90 " pdb=" C1' C A 90 " ideal model delta sinusoidal sigma weight residual 36.34 -42.55 78.89 1 3.10e+00 1.04e-01 8.07e+02 dihedral pdb=" C4' G A 818 " pdb=" C3' G A 818 " pdb=" C2' G A 818 " pdb=" C1' G A 818 " ideal model delta sinusoidal sigma weight residual 36.34 -41.12 77.46 1 3.10e+00 1.04e-01 7.82e+02 dihedral pdb=" C4' A A 182 " pdb=" C3' A A 182 " pdb=" C2' A A 182 " pdb=" C1' A A 182 " ideal model delta sinusoidal sigma weight residual 36.34 -39.92 76.26 1 3.10e+00 1.04e-01 7.62e+02 ... (remaining 19972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4705 0.082 - 0.164: 968 0.164 - 0.246: 1097 0.246 - 0.327: 274 0.327 - 0.409: 14 Chirality restraints: 7058 Sorted by residual: chirality pdb=" CA ASN D 89 " pdb=" N ASN D 89 " pdb=" C ASN D 89 " pdb=" CB ASN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN T 52 " pdb=" N ASN T 52 " pdb=" C ASN T 52 " pdb=" CB ASN T 52 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' G A 529 " pdb=" C3' G A 529 " pdb=" O2' G A 529 " pdb=" C1' G A 529 " both_signs ideal model delta sigma weight residual False -2.79 -2.41 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 7055 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.096 2.00e-02 2.50e+03 1.84e-01 1.10e+03 pdb=" N9 2MG A1516 " 0.009 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.089 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.121 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.035 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.011 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.086 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.093 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.182 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.265 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.157 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.053 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.512 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.134 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" N6 MA6 A1519 " -0.378 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.122 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.124 2.00e-02 2.50e+03 2.04e-01 4.17e+02 pdb=" N6 MA6 A1518 " -0.354 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.117 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.113 2.00e-02 2.50e+03 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 642 2.46 - 3.07: 26291 3.07 - 3.68: 78364 3.68 - 4.29: 102241 4.29 - 4.90: 134526 Nonbonded interactions: 342064 Sorted by model distance: nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1625 " model vdw 1.852 2.170 nonbonded pdb=" OP2 A A 53 " pdb="MG MG A1613 " model vdw 1.883 2.170 nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1625 " model vdw 1.890 2.170 nonbonded pdb=" O3' C A1521 " pdb="MG MG A1622 " model vdw 1.899 2.170 nonbonded pdb=" OP1 A A 547 " pdb="MG MG A1614 " model vdw 1.909 2.170 ... (remaining 342059 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 41.750 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.010 0.138 37176 Z= 0.609 Angle : 1.279 13.234 55425 Z= 0.685 Chirality : 0.112 0.409 7058 Planarity : 0.008 0.218 3112 Dihedral : 22.295 102.966 17217 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 43.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1458 helix: -0.77 (0.23), residues: 495 sheet: -1.05 (0.32), residues: 250 loop : -1.55 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG V 31 TYR 0.016 0.002 TYR L 95 PHE 0.023 0.002 PHE X 94 TRP 0.018 0.004 TRP F 42 HIS 0.011 0.002 HIS Q 47 Details of bonding type rmsd/Z covalent geometry : bond 0.01008 / 0.61 (37175) covalent geometry : angle 1.27859 / 0.68 (55425) hydrogen bonds : bond 0.34715 / 17.95 ( 1203) hydrogen bonds : angle 11.45922 / 4.62 ( 2323) Misc. bond : bond 0.00210 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7819 (mmmt) REVERT: D 51 TYR cc_start: 0.9026 (t80) cc_final: 0.8715 (t80) REVERT: D 71 GLN cc_start: 0.9255 (tt0) cc_final: 0.8881 (tp40) REVERT: D 72 PHE cc_start: 0.9611 (t80) cc_final: 0.9052 (t80) REVERT: D 74 ASN cc_start: 0.9073 (m-40) cc_final: 0.8821 (m110) REVERT: D 103 TYR cc_start: 0.8538 (t80) cc_final: 0.8125 (t80) REVERT: D 204 TYR cc_start: 0.8560 (m-80) cc_final: 0.7993 (m-80) REVERT: E 13 GLU cc_start: 0.9353 (pm20) cc_final: 0.9137 (pm20) REVERT: E 14 LYS cc_start: 0.8985 (tttm) cc_final: 0.8593 (mtmm) REVERT: E 30 ILE cc_start: 0.9048 (mm) cc_final: 0.8667 (mm) REVERT: E 31 PHE cc_start: 0.9383 (m-80) cc_final: 0.8994 (m-10) REVERT: E 62 LYS cc_start: 0.9426 (mtmt) cc_final: 0.9181 (mmtt) REVERT: E 68 ARG cc_start: 0.9299 (mmt-90) cc_final: 0.8674 (mmm160) REVERT: E 71 MET cc_start: 0.7894 (mtp) cc_final: 0.7054 (mtp) REVERT: F 13 ASP cc_start: 0.9397 (p0) cc_final: 0.9052 (p0) REVERT: F 14 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8411 (tm-30) REVERT: F 54 LEU cc_start: 0.9066 (mt) cc_final: 0.8776 (mt) REVERT: F 88 MET cc_start: 0.8628 (tmm) cc_final: 0.7361 (tmm) REVERT: F 89 VAL cc_start: 0.9233 (t) cc_final: 0.8992 (t) REVERT: F 90 MET cc_start: 0.8825 (mtm) cc_final: 0.8569 (tpp) REVERT: F 102 MET cc_start: 0.9000 (mmp) cc_final: 0.8768 (mmp) REVERT: H 39 VAL cc_start: 0.9608 (t) cc_final: 0.9173 (t) REVERT: H 45 PHE cc_start: 0.8580 (m-80) cc_final: 0.6931 (m-80) REVERT: H 59 LEU cc_start: 0.9302 (tp) cc_final: 0.9047 (tp) REVERT: H 89 LYS cc_start: 0.8915 (ptmm) cc_final: 0.8668 (ptpp) REVERT: H 113 ASP cc_start: 0.9307 (p0) cc_final: 0.8995 (p0) REVERT: H 121 LEU cc_start: 0.8960 (mt) cc_final: 0.8684 (tt) REVERT: H 125 ILE cc_start: 0.9417 (mt) cc_final: 0.9144 (mp) REVERT: H 126 ILE cc_start: 0.9629 (mm) cc_final: 0.9139 (mt) REVERT: K 38 GLN cc_start: 0.9147 (mt0) cc_final: 0.8936 (pp30) REVERT: K 79 ILE cc_start: 0.8899 (mt) cc_final: 0.8274 (mp) REVERT: K 85 MET cc_start: 0.8783 (mtp) cc_final: 0.8440 (mpp) REVERT: L 112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8677 (mp10) REVERT: O 65 LYS cc_start: 0.9651 (mttt) cc_final: 0.9357 (mmtt) REVERT: O 87 LEU cc_start: 0.9079 (mt) cc_final: 0.8784 (mt) REVERT: P 3 THR cc_start: 0.8225 (t) cc_final: 0.7973 (p) REVERT: P 12 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8368 (ttpp) REVERT: P 75 ILE cc_start: 0.9681 (mp) cc_final: 0.9256 (tp) REVERT: Q 15 ASP cc_start: 0.9008 (p0) cc_final: 0.8679 (p0) REVERT: Q 55 ILE cc_start: 0.8609 (pt) cc_final: 0.8038 (mp) REVERT: Q 57 ASP cc_start: 0.8769 (m-30) cc_final: 0.8527 (m-30) REVERT: Q 69 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8719 (ttpt) REVERT: R 22 ASP cc_start: 0.7839 (t0) cc_final: 0.7586 (t0) REVERT: R 23 TYR cc_start: 0.9260 (p90) cc_final: 0.8921 (p90) REVERT: R 60 LYS cc_start: 0.9435 (mttt) cc_final: 0.9163 (mtpp) REVERT: R 61 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8373 (mmt90) REVERT: T 27 MET cc_start: 0.9523 (tmm) cc_final: 0.9013 (tmm) REVERT: T 86 LEU cc_start: 0.8433 (mm) cc_final: 0.8232 (mm) REVERT: V 16 GLN cc_start: 0.9249 (mt0) cc_final: 0.8645 (mp10) REVERT: V 42 GLU cc_start: 0.8711 (tp30) cc_final: 0.8392 (mm-30) REVERT: X 30 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6971 (tpt90) REVERT: X 62 LEU cc_start: 0.9180 (tp) cc_final: 0.8548 (pp) REVERT: X 66 ASP cc_start: 0.8691 (t0) cc_final: 0.8216 (t0) REVERT: X 73 ASN cc_start: 0.9191 (t0) cc_final: 0.8547 (m-40) REVERT: X 145 ASN cc_start: 0.9039 (t0) cc_final: 0.8648 (t0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2507 time to fit residues: 160.4267 Evaluate side-chains 265 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 36 GLN E 70 ASN E 73 ASN E 83 HIS L 5 ASN L 72 HIS O 37 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN R 52 GLN V 16 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN X 140 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.025604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.021203 restraints weight = 516697.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.022002 restraints weight = 221051.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.022494 restraints weight = 127110.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022797 restraints weight = 86872.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.023013 restraints weight = 67211.483| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 37176 Z= 0.251 Angle : 1.503 24.105 55425 Z= 0.600 Chirality : 0.124 1.635 7058 Planarity : 0.006 0.080 3112 Dihedral : 20.239 164.150 14314 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.24 % Allowed : 4.15 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.21), residues: 1458 helix: -0.61 (0.21), residues: 535 sheet: -0.86 (0.30), residues: 277 loop : -1.14 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.023 0.002 TYR D 76 PHE 0.032 0.002 PHE H 45 TRP 0.013 0.002 TRP K 44 HIS 0.006 0.002 HIS O 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 (37175) covalent geometry : angle 1.50307 / 0.60 (55425) hydrogen bonds : bond 0.15304 / 7.95 ( 1203) hydrogen bonds : angle 5.67675 / 2.25 ( 2323) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 350 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.8979 (m-80) cc_final: 0.8720 (m-80) REVERT: D 51 TYR cc_start: 0.9162 (t80) cc_final: 0.8723 (t80) REVERT: D 71 GLN cc_start: 0.9128 (tt0) cc_final: 0.8340 (tp-100) REVERT: D 72 PHE cc_start: 0.9657 (t80) cc_final: 0.9125 (t80) REVERT: D 74 ASN cc_start: 0.9049 (m-40) cc_final: 0.8809 (m110) REVERT: D 75 TYR cc_start: 0.8898 (m-80) cc_final: 0.7921 (m-80) REVERT: D 103 TYR cc_start: 0.8797 (t80) cc_final: 0.8376 (t80) REVERT: D 140 ASN cc_start: 0.9586 (m-40) cc_final: 0.9364 (m-40) REVERT: E 71 MET cc_start: 0.7819 (mtp) cc_final: 0.6475 (mtp) REVERT: E 96 MET cc_start: 0.9287 (mmt) cc_final: 0.9010 (mmp) REVERT: F 16 GLU cc_start: 0.8989 (pm20) cc_final: 0.8783 (pm20) REVERT: F 21 MET cc_start: 0.9276 (ptm) cc_final: 0.8906 (ptm) REVERT: F 62 MET cc_start: 0.8553 (mpp) cc_final: 0.8172 (mpp) REVERT: F 88 MET cc_start: 0.8173 (tmm) cc_final: 0.7162 (tmm) REVERT: H 5 ASP cc_start: 0.8683 (t70) cc_final: 0.8394 (t0) REVERT: H 7 ILE cc_start: 0.9626 (mm) cc_final: 0.9342 (mp) REVERT: H 27 MET cc_start: 0.8616 (pmm) cc_final: 0.8326 (pmm) REVERT: H 86 TYR cc_start: 0.8494 (m-80) cc_final: 0.8273 (m-80) REVERT: H 99 LEU cc_start: 0.9316 (mp) cc_final: 0.9056 (mt) REVERT: H 113 ASP cc_start: 0.9242 (p0) cc_final: 0.9028 (p0) REVERT: H 121 LEU cc_start: 0.8917 (mt) cc_final: 0.8428 (tt) REVERT: L 66 TYR cc_start: 0.9282 (t80) cc_final: 0.8954 (t80) REVERT: L 112 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8706 (mp10) REVERT: O 87 LEU cc_start: 0.9149 (mt) cc_final: 0.8922 (mt) REVERT: P 12 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8002 (tmmt) REVERT: P 18 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8247 (mp10) REVERT: P 56 ARG cc_start: 0.9611 (tpm170) cc_final: 0.9034 (mmm160) REVERT: Q 15 ASP cc_start: 0.8785 (p0) cc_final: 0.8498 (p0) REVERT: Q 17 MET cc_start: 0.8778 (mpp) cc_final: 0.8339 (mpp) REVERT: Q 57 ASP cc_start: 0.8661 (m-30) cc_final: 0.8400 (m-30) REVERT: T 27 MET cc_start: 0.9507 (tmm) cc_final: 0.9253 (tmm) REVERT: T 51 PHE cc_start: 0.9302 (t80) cc_final: 0.9062 (t80) REVERT: V 16 GLN cc_start: 0.9151 (mt0) cc_final: 0.8435 (mp10) REVERT: V 43 MET cc_start: 0.8593 (mmt) cc_final: 0.8325 (mmm) REVERT: V 51 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8272 (mmtm) REVERT: V 62 GLU cc_start: 0.8777 (tp30) cc_final: 0.8332 (tp30) REVERT: X 37 ARG cc_start: 0.9410 (mtm180) cc_final: 0.9118 (ptp90) REVERT: X 62 LEU cc_start: 0.9309 (tp) cc_final: 0.8894 (pp) REVERT: X 66 ASP cc_start: 0.8780 (t0) cc_final: 0.8409 (m-30) REVERT: X 91 TYR cc_start: 0.9581 (m-80) cc_final: 0.9245 (m-80) REVERT: X 109 ASN cc_start: 0.8659 (p0) cc_final: 0.8281 (p0) outliers start: 3 outliers final: 1 residues processed: 352 average time/residue: 0.2308 time to fit residues: 126.5196 Evaluate side-chains 253 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [225, 244, 30, 153, 139, 165, 128, 167, 230, 108, 148] chunk 225 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN V 58 ASN ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.025743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.021351 restraints weight = 512937.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.022154 restraints weight = 218788.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.022647 restraints weight = 125553.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.022962 restraints weight = 85746.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.023170 restraints weight = 65826.953| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 37176 Z= 0.241 Angle : 1.177 17.491 55425 Z= 0.477 Chirality : 0.088 0.808 7058 Planarity : 0.005 0.080 3112 Dihedral : 20.117 177.891 14314 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.24 % Allowed : 4.80 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1458 helix: -0.29 (0.21), residues: 540 sheet: -0.85 (0.30), residues: 275 loop : -1.00 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 84 TYR 0.039 0.002 TYR V 49 PHE 0.019 0.002 PHE F 8 TRP 0.011 0.002 TRP P 60 HIS 0.009 0.002 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (37175) covalent geometry : angle 1.17684 / 0.48 (55425) hydrogen bonds : bond 0.13002 / 6.86 ( 1203) hydrogen bonds : angle 5.16320 / 2.06 ( 2323) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 326 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.9073 (m-80) cc_final: 0.8737 (m-80) REVERT: D 51 TYR cc_start: 0.9164 (t80) cc_final: 0.8656 (t80) REVERT: D 71 GLN cc_start: 0.9085 (tt0) cc_final: 0.8296 (tp-100) REVERT: D 72 PHE cc_start: 0.9626 (t80) cc_final: 0.8831 (t80) REVERT: D 74 ASN cc_start: 0.9031 (m-40) cc_final: 0.8806 (m110) REVERT: D 75 TYR cc_start: 0.8929 (m-80) cc_final: 0.8018 (m-80) REVERT: D 103 TYR cc_start: 0.8772 (t80) cc_final: 0.8479 (t80) REVERT: D 140 ASN cc_start: 0.9596 (m-40) cc_final: 0.9369 (m-40) REVERT: E 41 ASP cc_start: 0.7336 (m-30) cc_final: 0.6767 (m-30) REVERT: E 71 MET cc_start: 0.7951 (mtp) cc_final: 0.6010 (ttm) REVERT: F 1 MET cc_start: 0.7541 (ptm) cc_final: 0.7231 (ptm) REVERT: F 9 MET cc_start: 0.8704 (mmm) cc_final: 0.8418 (mmm) REVERT: F 88 MET cc_start: 0.7910 (tmm) cc_final: 0.6671 (tmm) REVERT: F 89 VAL cc_start: 0.9265 (t) cc_final: 0.9050 (t) REVERT: F 102 MET cc_start: 0.9123 (mpp) cc_final: 0.8879 (mpp) REVERT: H 5 ASP cc_start: 0.8587 (t70) cc_final: 0.8359 (t0) REVERT: H 7 ILE cc_start: 0.9666 (mm) cc_final: 0.9418 (mp) REVERT: H 10 MET cc_start: 0.9570 (tmm) cc_final: 0.9127 (tmm) REVERT: H 11 LEU cc_start: 0.9616 (mt) cc_final: 0.9373 (mt) REVERT: H 27 MET cc_start: 0.8717 (pmm) cc_final: 0.8271 (pmm) REVERT: H 42 GLU cc_start: 0.9618 (OUTLIER) cc_final: 0.9308 (mp0) REVERT: H 45 PHE cc_start: 0.7754 (m-10) cc_final: 0.7361 (m-10) REVERT: K 109 ASN cc_start: 0.8173 (t0) cc_final: 0.7926 (t0) REVERT: L 38 TYR cc_start: 0.9358 (p90) cc_final: 0.9128 (p90) REVERT: L 66 TYR cc_start: 0.9283 (t80) cc_final: 0.9080 (t80) REVERT: L 73 ASN cc_start: 0.9258 (m-40) cc_final: 0.8753 (p0) REVERT: L 103 ASP cc_start: 0.8692 (t70) cc_final: 0.8286 (t0) REVERT: L 112 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8666 (mp10) REVERT: O 68 ASP cc_start: 0.9604 (m-30) cc_final: 0.9370 (m-30) REVERT: O 87 LEU cc_start: 0.9205 (mt) cc_final: 0.8995 (mt) REVERT: P 12 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8283 (ttpp) REVERT: P 18 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8431 (mp10) REVERT: P 52 LEU cc_start: 0.8854 (mt) cc_final: 0.8225 (pt) REVERT: Q 15 ASP cc_start: 0.8788 (p0) cc_final: 0.8372 (p0) REVERT: Q 17 MET cc_start: 0.8741 (mpp) cc_final: 0.8439 (mpp) REVERT: Q 25 ILE cc_start: 0.9151 (mp) cc_final: 0.8657 (mp) REVERT: Q 27 ARG cc_start: 0.8903 (ptt-90) cc_final: 0.8523 (ptt-90) REVERT: Q 42 THR cc_start: 0.8487 (p) cc_final: 0.6507 (p) REVERT: Q 55 ILE cc_start: 0.8197 (pt) cc_final: 0.7570 (mp) REVERT: Q 57 ASP cc_start: 0.8620 (m-30) cc_final: 0.8315 (m-30) REVERT: T 24 ARG cc_start: 0.9011 (mtp180) cc_final: 0.8631 (mtp180) REVERT: T 27 MET cc_start: 0.9506 (tmm) cc_final: 0.9253 (tmm) REVERT: T 54 MET cc_start: 0.8921 (tmm) cc_final: 0.8719 (tmm) REVERT: V 51 LYS cc_start: 0.8493 (mmpt) cc_final: 0.8012 (mtpp) REVERT: X 37 ARG cc_start: 0.9423 (mtm180) cc_final: 0.9180 (ptp90) REVERT: X 91 TYR cc_start: 0.9599 (m-80) cc_final: 0.9137 (m-80) REVERT: X 100 THR cc_start: 0.9316 (m) cc_final: 0.8581 (m) REVERT: X 109 ASN cc_start: 0.8614 (p0) cc_final: 0.8208 (p0) REVERT: X 114 GLN cc_start: 0.9108 (pm20) cc_final: 0.8880 (tt0) outliers start: 3 outliers final: 1 residues processed: 328 average time/residue: 0.2274 time to fit residues: 116.9037 Evaluate side-chains 247 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [218, 220, 219, 19, 51, 38, 61, 119, 22, 86, 240] chunk 218 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN L 96 HIS ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 ASN ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.024783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.020417 restraints weight = 516473.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.021183 restraints weight = 220159.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.021664 restraints weight = 126175.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.021963 restraints weight = 85756.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.022145 restraints weight = 66580.326| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 37176 Z= 0.311 Angle : 1.195 16.152 55425 Z= 0.483 Chirality : 0.083 0.678 7058 Planarity : 0.005 0.050 3112 Dihedral : 19.981 177.572 14314 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1458 helix: -0.34 (0.20), residues: 548 sheet: -1.11 (0.29), residues: 287 loop : -1.14 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 20 TYR 0.026 0.002 TYR L 95 PHE 0.021 0.003 PHE T 31 TRP 0.011 0.002 TRP P 60 HIS 0.007 0.002 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.31 (37175) covalent geometry : angle 1.19488 / 0.48 (55425) hydrogen bonds : bond 0.13170 / 6.95 ( 1203) hydrogen bonds : angle 5.11076 / 2.04 ( 2323) Misc. bond : bond 0.00090 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 291 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 TYR cc_start: 0.9094 (t80) cc_final: 0.8778 (t80) REVERT: D 71 GLN cc_start: 0.9130 (tt0) cc_final: 0.8370 (tp-100) REVERT: D 72 PHE cc_start: 0.9694 (t80) cc_final: 0.9074 (t80) REVERT: D 75 TYR cc_start: 0.8882 (m-80) cc_final: 0.8034 (m-80) REVERT: D 140 ASN cc_start: 0.9602 (m-40) cc_final: 0.9373 (m-40) REVERT: E 41 ASP cc_start: 0.7479 (m-30) cc_final: 0.6847 (m-30) REVERT: E 71 MET cc_start: 0.8278 (mtp) cc_final: 0.6442 (mtp) REVERT: F 75 GLU cc_start: 0.9084 (pp20) cc_final: 0.8823 (pp20) REVERT: F 88 MET cc_start: 0.8493 (tmm) cc_final: 0.7623 (tmm) REVERT: F 98 GLU cc_start: 0.8977 (mp0) cc_final: 0.8709 (mp0) REVERT: F 102 MET cc_start: 0.9165 (mpp) cc_final: 0.8835 (mpp) REVERT: H 5 ASP cc_start: 0.8580 (t70) cc_final: 0.8310 (t0) REVERT: H 7 ILE cc_start: 0.9673 (mm) cc_final: 0.9437 (mp) REVERT: H 10 MET cc_start: 0.9561 (tmm) cc_final: 0.9210 (tmm) REVERT: H 11 LEU cc_start: 0.9660 (mt) cc_final: 0.9407 (mt) REVERT: H 27 MET cc_start: 0.8620 (pmm) cc_final: 0.8231 (pmm) REVERT: H 90 ASP cc_start: 0.9343 (p0) cc_final: 0.8628 (p0) REVERT: K 109 ASN cc_start: 0.8271 (t0) cc_final: 0.8054 (t0) REVERT: L 38 TYR cc_start: 0.9372 (p90) cc_final: 0.8846 (p90) REVERT: L 66 TYR cc_start: 0.9277 (t80) cc_final: 0.8699 (t80) REVERT: L 70 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8639 (mp0) REVERT: L 73 ASN cc_start: 0.9311 (m-40) cc_final: 0.8852 (p0) REVERT: L 103 ASP cc_start: 0.8905 (t70) cc_final: 0.8253 (t0) REVERT: L 112 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8651 (mp10) REVERT: O 87 LEU cc_start: 0.9079 (mt) cc_final: 0.8861 (mt) REVERT: P 18 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8387 (mp10) REVERT: P 26 ASN cc_start: 0.9357 (m-40) cc_final: 0.8710 (t0) REVERT: P 34 GLU cc_start: 0.9013 (pp20) cc_final: 0.8801 (pp20) REVERT: P 48 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7766 (tm-30) REVERT: Q 15 ASP cc_start: 0.8806 (p0) cc_final: 0.8459 (p0) REVERT: Q 17 MET cc_start: 0.8669 (mpp) cc_final: 0.8173 (mpp) REVERT: Q 25 ILE cc_start: 0.9107 (mp) cc_final: 0.8883 (mp) REVERT: Q 27 ARG cc_start: 0.9018 (ptt-90) cc_final: 0.8683 (ptt-90) REVERT: Q 55 ILE cc_start: 0.8224 (pt) cc_final: 0.7698 (mp) REVERT: R 29 LEU cc_start: 0.9546 (mm) cc_final: 0.9318 (mm) REVERT: T 24 ARG cc_start: 0.9109 (mtp180) cc_final: 0.8573 (mtt180) REVERT: T 27 MET cc_start: 0.9357 (tmm) cc_final: 0.9075 (tmm) REVERT: T 51 PHE cc_start: 0.9306 (t80) cc_final: 0.9027 (t80) REVERT: T 54 MET cc_start: 0.8918 (tmm) cc_final: 0.8713 (tmm) REVERT: V 51 LYS cc_start: 0.8607 (mmpt) cc_final: 0.8038 (mtpp) REVERT: X 1 MET cc_start: 0.0507 (mtt) cc_final: -0.0138 (mtt) REVERT: X 91 TYR cc_start: 0.9505 (m-80) cc_final: 0.8992 (m-80) REVERT: X 109 ASN cc_start: 0.8537 (p0) cc_final: 0.7980 (p0) outliers start: 3 outliers final: 0 residues processed: 291 average time/residue: 0.2235 time to fit residues: 102.1052 Evaluate side-chains 216 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [12, 94, 118, 189, 235, 158, 25, 104, 61, 4, 166] chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN D 126 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.025097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.020714 restraints weight = 511519.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.021494 restraints weight = 216612.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.021976 restraints weight = 124036.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.022278 restraints weight = 84759.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.022481 restraints weight = 65426.994| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 37176 Z= 0.267 Angle : 1.118 12.981 55425 Z= 0.453 Chirality : 0.080 0.699 7058 Planarity : 0.005 0.064 3112 Dihedral : 19.942 179.360 14314 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1458 helix: -0.15 (0.21), residues: 551 sheet: -1.19 (0.28), residues: 311 loop : -1.13 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 128 TYR 0.027 0.002 TYR L 95 PHE 0.028 0.002 PHE F 8 TRP 0.014 0.002 TRP X 113 HIS 0.007 0.002 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.27 (37175) covalent geometry : angle 1.11817 / 0.45 (55425) hydrogen bonds : bond 0.12365 / 6.50 ( 1203) hydrogen bonds : angle 5.08243 / 2.03 ( 2323) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 TYR cc_start: 0.9153 (t80) cc_final: 0.8722 (t80) REVERT: D 71 GLN cc_start: 0.9121 (tt0) cc_final: 0.8365 (tp-100) REVERT: D 72 PHE cc_start: 0.9683 (t80) cc_final: 0.8881 (t80) REVERT: D 75 TYR cc_start: 0.8895 (m-80) cc_final: 0.8056 (m-80) REVERT: D 103 TYR cc_start: 0.8694 (t80) cc_final: 0.8303 (t80) REVERT: D 140 ASN cc_start: 0.9600 (m-40) cc_final: 0.9368 (m-40) REVERT: E 41 ASP cc_start: 0.7423 (m-30) cc_final: 0.7071 (m-30) REVERT: E 71 MET cc_start: 0.8364 (mtp) cc_final: 0.6934 (ttp) REVERT: E 96 MET cc_start: 0.9275 (mmp) cc_final: 0.9063 (mmp) REVERT: F 75 GLU cc_start: 0.9083 (pp20) cc_final: 0.8811 (pp20) REVERT: F 88 MET cc_start: 0.8252 (tmm) cc_final: 0.7307 (tmm) REVERT: F 98 GLU cc_start: 0.8969 (mp0) cc_final: 0.8679 (mp0) REVERT: F 102 MET cc_start: 0.9213 (mpp) cc_final: 0.8987 (mpp) REVERT: H 10 MET cc_start: 0.9551 (tmm) cc_final: 0.9209 (tmm) REVERT: H 11 LEU cc_start: 0.9678 (mt) cc_final: 0.9447 (mt) REVERT: H 27 MET cc_start: 0.8786 (pmm) cc_final: 0.8325 (pmm) REVERT: H 125 ILE cc_start: 0.9296 (mp) cc_final: 0.9092 (mp) REVERT: K 109 ASN cc_start: 0.8249 (t0) cc_final: 0.8004 (t0) REVERT: L 38 TYR cc_start: 0.9387 (p90) cc_final: 0.8820 (p90) REVERT: L 73 ASN cc_start: 0.9291 (m-40) cc_final: 0.8860 (p0) REVERT: L 103 ASP cc_start: 0.8859 (t70) cc_final: 0.8021 (t0) REVERT: L 112 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8646 (mp10) REVERT: O 87 LEU cc_start: 0.9149 (mt) cc_final: 0.8915 (mt) REVERT: P 18 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8386 (mp10) REVERT: P 56 ARG cc_start: 0.9542 (tpm170) cc_final: 0.9220 (mmm160) REVERT: Q 8 LEU cc_start: 0.9577 (tp) cc_final: 0.9061 (tp) REVERT: Q 15 ASP cc_start: 0.8787 (p0) cc_final: 0.8493 (p0) REVERT: Q 17 MET cc_start: 0.8731 (mpp) cc_final: 0.8282 (mpp) REVERT: Q 25 ILE cc_start: 0.9101 (mp) cc_final: 0.8766 (mp) REVERT: Q 27 ARG cc_start: 0.8975 (ptt-90) cc_final: 0.8618 (ptt-90) REVERT: Q 42 THR cc_start: 0.8903 (p) cc_final: 0.7562 (p) REVERT: Q 55 ILE cc_start: 0.8202 (pt) cc_final: 0.7694 (mp) REVERT: R 29 LEU cc_start: 0.9501 (mm) cc_final: 0.9246 (mm) REVERT: T 24 ARG cc_start: 0.9154 (mtp180) cc_final: 0.8649 (mtp180) REVERT: T 27 MET cc_start: 0.9311 (tmm) cc_final: 0.9023 (tmm) REVERT: T 51 PHE cc_start: 0.9356 (t80) cc_final: 0.9119 (t80) REVERT: V 15 MET cc_start: 0.8735 (mmp) cc_final: 0.8527 (mtp) REVERT: V 49 TYR cc_start: 0.8616 (m-10) cc_final: 0.8312 (m-10) REVERT: X 1 MET cc_start: 0.0368 (mtt) cc_final: -0.0227 (mtt) REVERT: X 91 TYR cc_start: 0.9533 (m-80) cc_final: 0.9006 (m-80) REVERT: X 109 ASN cc_start: 0.8681 (p0) cc_final: 0.8058 (p0) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.2274 time to fit residues: 101.8191 Evaluate side-chains 215 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [170, 192, 180, 63, 121, 205, 219, 70, 21, 105, 107] chunk 170 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 63 optimal weight: 10.9990 chunk 121 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN D 126 ASN F 17 GLN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.024935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.020577 restraints weight = 513333.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.021350 restraints weight = 216542.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.021825 restraints weight = 123397.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.022128 restraints weight = 84047.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022322 restraints weight = 65180.815| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 37176 Z= 0.277 Angle : 1.116 12.874 55425 Z= 0.452 Chirality : 0.079 0.743 7058 Planarity : 0.005 0.048 3112 Dihedral : 19.918 179.640 14314 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1458 helix: -0.30 (0.21), residues: 553 sheet: -1.32 (0.28), residues: 285 loop : -1.26 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 63 TYR 0.027 0.002 TYR L 95 PHE 0.020 0.002 PHE F 78 TRP 0.013 0.002 TRP X 113 HIS 0.009 0.002 HIS O 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.28 (37175) covalent geometry : angle 1.11640 / 0.45 (55425) hydrogen bonds : bond 0.12270 / 6.43 ( 1203) hydrogen bonds : angle 5.04382 / 2.01 ( 2323) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.6936 (t80) cc_final: 0.6703 (t80) REVERT: D 71 GLN cc_start: 0.9084 (tt0) cc_final: 0.8345 (tp-100) REVERT: D 72 PHE cc_start: 0.9678 (t80) cc_final: 0.9012 (t80) REVERT: D 75 TYR cc_start: 0.8897 (m-80) cc_final: 0.8069 (m-80) REVERT: D 103 TYR cc_start: 0.8763 (t80) cc_final: 0.8389 (t80) REVERT: E 41 ASP cc_start: 0.7290 (m-30) cc_final: 0.6562 (m-30) REVERT: E 71 MET cc_start: 0.8444 (mtp) cc_final: 0.6636 (mtp) REVERT: E 86 LYS cc_start: 0.8684 (tptp) cc_final: 0.8462 (tptt) REVERT: E 96 MET cc_start: 0.9399 (mmp) cc_final: 0.9069 (mmp) REVERT: F 75 GLU cc_start: 0.9068 (pp20) cc_final: 0.8812 (pp20) REVERT: F 88 MET cc_start: 0.8099 (tmm) cc_final: 0.7178 (tmm) REVERT: F 102 MET cc_start: 0.9211 (mpp) cc_final: 0.8988 (mpp) REVERT: H 10 MET cc_start: 0.9544 (tmm) cc_final: 0.9265 (tmm) REVERT: H 11 LEU cc_start: 0.9694 (mt) cc_final: 0.9430 (mt) REVERT: H 27 MET cc_start: 0.8692 (pmm) cc_final: 0.8220 (pmm) REVERT: H 107 SER cc_start: 0.9405 (m) cc_final: 0.8849 (t) REVERT: H 125 ILE cc_start: 0.9261 (mp) cc_final: 0.9020 (mp) REVERT: L 38 TYR cc_start: 0.9361 (p90) cc_final: 0.8705 (p90) REVERT: L 73 ASN cc_start: 0.9265 (m-40) cc_final: 0.8912 (p0) REVERT: L 112 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8658 (mp10) REVERT: P 18 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8473 (mp10) REVERT: P 34 GLU cc_start: 0.8996 (pp20) cc_final: 0.8771 (pp20) REVERT: Q 11 ARG cc_start: 0.9286 (ppt170) cc_final: 0.9062 (ttp80) REVERT: Q 15 ASP cc_start: 0.8807 (p0) cc_final: 0.8459 (p0) REVERT: Q 17 MET cc_start: 0.8752 (mpp) cc_final: 0.8348 (mpp) REVERT: Q 25 ILE cc_start: 0.9049 (mp) cc_final: 0.8708 (mp) REVERT: Q 27 ARG cc_start: 0.8974 (ptt-90) cc_final: 0.8601 (ptt-90) REVERT: Q 55 ILE cc_start: 0.8220 (pt) cc_final: 0.7681 (mp) REVERT: R 29 LEU cc_start: 0.9481 (mm) cc_final: 0.9257 (mm) REVERT: T 24 ARG cc_start: 0.9163 (mtp180) cc_final: 0.8665 (mtp180) REVERT: T 27 MET cc_start: 0.9316 (tmm) cc_final: 0.8746 (tmm) REVERT: X 1 MET cc_start: 0.0506 (mtt) cc_final: -0.0069 (mtt) REVERT: X 91 TYR cc_start: 0.9567 (m-80) cc_final: 0.9014 (m-80) REVERT: X 109 ASN cc_start: 0.8739 (p0) cc_final: 0.8288 (p0) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.2125 time to fit residues: 93.8522 Evaluate side-chains 211 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [196, 179, 154, 147, 101, 65, 242, 188, 52, 16, 218] chunk 196 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 58 ASN ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.025526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.021128 restraints weight = 506045.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.021910 restraints weight = 216478.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.022411 restraints weight = 123684.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.022719 restraints weight = 83875.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.022912 restraints weight = 64391.320| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37176 Z= 0.220 Angle : 1.058 12.881 55425 Z= 0.431 Chirality : 0.077 0.723 7058 Planarity : 0.005 0.045 3112 Dihedral : 19.824 179.557 14314 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1458 helix: -0.18 (0.21), residues: 560 sheet: -1.32 (0.28), residues: 296 loop : -1.28 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 45 TYR 0.024 0.002 TYR L 95 PHE 0.024 0.002 PHE F 8 TRP 0.015 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.22 (37175) covalent geometry : angle 1.05814 / 0.43 (55425) hydrogen bonds : bond 0.11721 / 6.13 ( 1203) hydrogen bonds : angle 4.99870 / 2.00 ( 2323) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 TYR cc_start: 0.6765 (t80) cc_final: 0.6562 (t80) REVERT: D 71 GLN cc_start: 0.9064 (tt0) cc_final: 0.8337 (tp-100) REVERT: D 72 PHE cc_start: 0.9686 (t80) cc_final: 0.8864 (t80) REVERT: D 75 TYR cc_start: 0.8884 (m-80) cc_final: 0.8025 (m-80) REVERT: D 103 TYR cc_start: 0.8754 (t80) cc_final: 0.8425 (t80) REVERT: E 41 ASP cc_start: 0.7296 (m-30) cc_final: 0.6959 (m-30) REVERT: E 71 MET cc_start: 0.8650 (mtp) cc_final: 0.7459 (ttp) REVERT: F 6 ILE cc_start: 0.9369 (mp) cc_final: 0.9061 (mp) REVERT: F 75 GLU cc_start: 0.9026 (pp20) cc_final: 0.8746 (pp20) REVERT: F 88 MET cc_start: 0.7980 (tmm) cc_final: 0.7236 (tmm) REVERT: F 91 ARG cc_start: 0.9235 (mtp180) cc_final: 0.8991 (mmm-85) REVERT: F 98 GLU cc_start: 0.8898 (mp0) cc_final: 0.8662 (mp0) REVERT: H 10 MET cc_start: 0.9519 (tmm) cc_final: 0.9228 (tmm) REVERT: H 27 MET cc_start: 0.8838 (pmm) cc_final: 0.8483 (pmm) REVERT: H 107 SER cc_start: 0.9384 (m) cc_final: 0.8971 (p) REVERT: H 113 ASP cc_start: 0.9225 (p0) cc_final: 0.8881 (p0) REVERT: L 38 TYR cc_start: 0.9422 (p90) cc_final: 0.8801 (p90) REVERT: L 73 ASN cc_start: 0.9278 (m-40) cc_final: 0.8988 (p0) REVERT: L 112 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8644 (mp10) REVERT: O 65 LYS cc_start: 0.9614 (mtpt) cc_final: 0.9299 (ptpt) REVERT: P 17 TYR cc_start: 0.8489 (m-80) cc_final: 0.7852 (m-80) REVERT: P 18 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8479 (mp10) REVERT: P 34 GLU cc_start: 0.8997 (pp20) cc_final: 0.8792 (pp20) REVERT: P 76 LYS cc_start: 0.9600 (tmtt) cc_final: 0.9327 (tmtt) REVERT: Q 15 ASP cc_start: 0.8775 (p0) cc_final: 0.8403 (p0) REVERT: Q 17 MET cc_start: 0.8806 (mpp) cc_final: 0.8441 (mpp) REVERT: Q 27 ARG cc_start: 0.8952 (ptt-90) cc_final: 0.8596 (ptt-90) REVERT: Q 42 THR cc_start: 0.8888 (p) cc_final: 0.7595 (p) REVERT: Q 55 ILE cc_start: 0.8256 (pt) cc_final: 0.7712 (mp) REVERT: R 29 LEU cc_start: 0.9421 (mm) cc_final: 0.9197 (mm) REVERT: T 27 MET cc_start: 0.9327 (tmm) cc_final: 0.9046 (tmm) REVERT: X 1 MET cc_start: 0.0546 (mtt) cc_final: 0.0007 (mtt) REVERT: X 91 TYR cc_start: 0.9573 (m-80) cc_final: 0.9068 (m-80) REVERT: X 109 ASN cc_start: 0.8647 (p0) cc_final: 0.8218 (p0) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2101 time to fit residues: 95.5089 Evaluate side-chains 219 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [48, 102, 100, 36, 234, 89, 21, 32, 148, 107, 46] chunk 48 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.024624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.020310 restraints weight = 518560.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.021080 restraints weight = 217026.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.021560 restraints weight = 123451.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.021853 restraints weight = 83876.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.022042 restraints weight = 64605.209| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 37176 Z= 0.326 Angle : 1.148 13.054 55425 Z= 0.466 Chirality : 0.078 0.720 7058 Planarity : 0.005 0.049 3112 Dihedral : 19.908 178.702 14314 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1458 helix: -0.31 (0.21), residues: 557 sheet: -1.37 (0.29), residues: 285 loop : -1.24 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 20 TYR 0.027 0.002 TYR L 95 PHE 0.024 0.003 PHE X 150 TRP 0.019 0.003 TRP F 42 HIS 0.006 0.002 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.33 (37175) covalent geometry : angle 1.14803 / 0.47 (55425) hydrogen bonds : bond 0.12571 / 6.59 ( 1203) hydrogen bonds : angle 5.20234 / 2.09 ( 2323) Misc. bond : bond 0.00108 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9089 (tt0) cc_final: 0.8342 (tp-100) REVERT: D 72 PHE cc_start: 0.9679 (t80) cc_final: 0.9025 (t80) REVERT: D 75 TYR cc_start: 0.8891 (m-80) cc_final: 0.8019 (m-80) REVERT: D 103 TYR cc_start: 0.8738 (t80) cc_final: 0.8409 (t80) REVERT: D 124 MET cc_start: 0.7492 (mmm) cc_final: 0.7059 (mmm) REVERT: E 41 ASP cc_start: 0.7357 (m-30) cc_final: 0.6732 (m-30) REVERT: E 64 MET cc_start: 0.9555 (ptp) cc_final: 0.9304 (ptp) REVERT: E 71 MET cc_start: 0.8568 (mtp) cc_final: 0.6880 (mtp) REVERT: E 111 MET cc_start: 0.9297 (ttp) cc_final: 0.8912 (ttp) REVERT: F 75 GLU cc_start: 0.9033 (pp20) cc_final: 0.8763 (pp20) REVERT: F 88 MET cc_start: 0.8122 (tmm) cc_final: 0.7383 (tmm) REVERT: F 98 GLU cc_start: 0.9042 (mp0) cc_final: 0.8830 (mp0) REVERT: H 10 MET cc_start: 0.9489 (tmm) cc_final: 0.9238 (ppp) REVERT: H 27 MET cc_start: 0.8703 (pmm) cc_final: 0.8384 (pmm) REVERT: H 107 SER cc_start: 0.9424 (m) cc_final: 0.8887 (t) REVERT: H 113 ASP cc_start: 0.9232 (p0) cc_final: 0.8891 (p0) REVERT: L 38 TYR cc_start: 0.9386 (p90) cc_final: 0.8693 (p90) REVERT: L 73 ASN cc_start: 0.9343 (m-40) cc_final: 0.9040 (p0) REVERT: L 93 VAL cc_start: 0.8755 (t) cc_final: 0.8493 (p) REVERT: L 112 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8670 (mp10) REVERT: O 87 LEU cc_start: 0.9199 (mt) cc_final: 0.8995 (mt) REVERT: P 18 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8476 (mp10) REVERT: P 76 LYS cc_start: 0.9579 (tmtt) cc_final: 0.9340 (tmtt) REVERT: Q 15 ASP cc_start: 0.8802 (p0) cc_final: 0.8480 (p0) REVERT: Q 17 MET cc_start: 0.8818 (mpp) cc_final: 0.8496 (mpp) REVERT: Q 27 ARG cc_start: 0.8992 (ptt-90) cc_final: 0.8643 (ptt-90) REVERT: Q 42 THR cc_start: 0.8947 (p) cc_final: 0.7878 (p) REVERT: Q 55 ILE cc_start: 0.8375 (pt) cc_final: 0.7833 (mp) REVERT: R 29 LEU cc_start: 0.9409 (mm) cc_final: 0.9198 (mm) REVERT: T 15 GLU cc_start: 0.9180 (tp30) cc_final: 0.8975 (tp30) REVERT: T 27 MET cc_start: 0.9268 (tmm) cc_final: 0.9062 (tmm) REVERT: T 54 MET cc_start: 0.9023 (tmm) cc_final: 0.8820 (tmm) REVERT: X 1 MET cc_start: 0.0615 (mtt) cc_final: 0.0259 (mtt) REVERT: X 91 TYR cc_start: 0.9592 (m-80) cc_final: 0.9091 (m-80) REVERT: X 109 ASN cc_start: 0.8727 (p0) cc_final: 0.8449 (p0) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2052 time to fit residues: 89.7115 Evaluate side-chains 209 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [117, 116, 240, 243, 47, 191, 8, 242, 71, 44, 55] chunk 117 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.024986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.020679 restraints weight = 512709.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.021440 restraints weight = 215842.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.021911 restraints weight = 123473.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.022210 restraints weight = 84675.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.022391 restraints weight = 65667.034| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 37176 Z= 0.254 Angle : 1.081 12.933 55425 Z= 0.440 Chirality : 0.076 0.707 7058 Planarity : 0.005 0.045 3112 Dihedral : 19.865 179.090 14314 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1458 helix: -0.24 (0.21), residues: 561 sheet: -1.40 (0.28), residues: 291 loop : -1.26 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.027 0.002 TYR L 95 PHE 0.019 0.002 PHE F 78 TRP 0.017 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 (37175) covalent geometry : angle 1.08131 / 0.44 (55425) hydrogen bonds : bond 0.11866 / 6.21 ( 1203) hydrogen bonds : angle 5.09157 / 2.04 ( 2323) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9059 (tt0) cc_final: 0.8331 (tp-100) REVERT: D 72 PHE cc_start: 0.9668 (t80) cc_final: 0.9003 (t80) REVERT: D 75 TYR cc_start: 0.8879 (m-80) cc_final: 0.7973 (m-80) REVERT: D 103 TYR cc_start: 0.8720 (t80) cc_final: 0.8409 (t80) REVERT: D 124 MET cc_start: 0.7672 (mmm) cc_final: 0.7249 (mmm) REVERT: D 140 ASN cc_start: 0.9511 (m-40) cc_final: 0.9107 (p0) REVERT: E 41 ASP cc_start: 0.7378 (m-30) cc_final: 0.7077 (m-30) REVERT: E 64 MET cc_start: 0.9546 (ptp) cc_final: 0.9304 (ptp) REVERT: E 71 MET cc_start: 0.8727 (mtp) cc_final: 0.7515 (ttp) REVERT: E 88 VAL cc_start: 0.9040 (t) cc_final: 0.8821 (t) REVERT: F 75 GLU cc_start: 0.9018 (pp20) cc_final: 0.8746 (pp20) REVERT: F 88 MET cc_start: 0.8077 (tmm) cc_final: 0.7217 (tmm) REVERT: H 10 MET cc_start: 0.9504 (tmm) cc_final: 0.9261 (tmm) REVERT: H 11 LEU cc_start: 0.9716 (mt) cc_final: 0.9447 (mt) REVERT: H 27 MET cc_start: 0.8774 (pmm) cc_final: 0.8441 (pmm) REVERT: H 80 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.8252 (mtp-110) REVERT: H 107 SER cc_start: 0.9447 (m) cc_final: 0.9032 (p) REVERT: H 113 ASP cc_start: 0.9191 (p0) cc_final: 0.8869 (p0) REVERT: L 38 TYR cc_start: 0.9373 (p90) cc_final: 0.9147 (p90) REVERT: L 73 ASN cc_start: 0.9332 (m-40) cc_final: 0.9016 (p0) REVERT: L 93 VAL cc_start: 0.8803 (t) cc_final: 0.8537 (p) REVERT: L 112 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8658 (mp10) REVERT: O 87 LEU cc_start: 0.9217 (mt) cc_final: 0.9008 (mt) REVERT: P 17 TYR cc_start: 0.8508 (m-80) cc_final: 0.7849 (m-80) REVERT: P 18 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8555 (mp10) REVERT: P 34 GLU cc_start: 0.8992 (pp20) cc_final: 0.8791 (pp20) REVERT: P 56 ARG cc_start: 0.9534 (tpm170) cc_final: 0.9197 (mmm160) REVERT: Q 15 ASP cc_start: 0.8778 (p0) cc_final: 0.8549 (p0) REVERT: Q 17 MET cc_start: 0.8852 (mpp) cc_final: 0.8481 (mpp) REVERT: Q 27 ARG cc_start: 0.8975 (ptt-90) cc_final: 0.8635 (ptt-90) REVERT: Q 42 THR cc_start: 0.8934 (p) cc_final: 0.7865 (p) REVERT: R 29 LEU cc_start: 0.9363 (mm) cc_final: 0.9137 (mm) REVERT: T 13 GLN cc_start: 0.9076 (pp30) cc_final: 0.8874 (pp30) REVERT: T 27 MET cc_start: 0.9202 (tmm) cc_final: 0.8982 (tmm) REVERT: T 28 MET cc_start: 0.9206 (tpt) cc_final: 0.8829 (mmt) REVERT: T 54 MET cc_start: 0.9037 (tmm) cc_final: 0.8806 (tmm) REVERT: T 79 LEU cc_start: 0.9338 (mt) cc_final: 0.9097 (mt) REVERT: X 1 MET cc_start: 0.0132 (mtt) cc_final: -0.0206 (mtt) REVERT: X 91 TYR cc_start: 0.9587 (m-80) cc_final: 0.9085 (m-80) REVERT: X 109 ASN cc_start: 0.8721 (p0) cc_final: 0.8464 (p0) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2086 time to fit residues: 93.2796 Evaluate side-chains 215 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [171, 84, 66, 47, 147, 113, 204, 226, 151, 211, 34] chunk 171 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 211 optimal weight: 0.0040 chunk 34 optimal weight: 9.9990 overall best weight: 4.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.025346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.020977 restraints weight = 512974.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.021753 restraints weight = 214856.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.022233 restraints weight = 122372.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.022540 restraints weight = 83769.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.022716 restraints weight = 64532.473| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 37176 Z= 0.228 Angle : 1.056 12.994 55425 Z= 0.430 Chirality : 0.075 0.757 7058 Planarity : 0.005 0.053 3112 Dihedral : 19.777 179.693 14314 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.21), residues: 1458 helix: -0.19 (0.21), residues: 562 sheet: -1.41 (0.29), residues: 292 loop : -1.34 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 20 TYR 0.025 0.002 TYR L 95 PHE 0.028 0.002 PHE F 8 TRP 0.016 0.002 TRP X 113 HIS 0.008 0.002 HIS F 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (37175) covalent geometry : angle 1.05551 / 0.43 (55425) hydrogen bonds : bond 0.11600 / 6.06 ( 1203) hydrogen bonds : angle 5.01434 / 2.01 ( 2323) Misc. bond : bond 0.00086 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.9053 (tt0) cc_final: 0.8313 (tp-100) REVERT: D 72 PHE cc_start: 0.9675 (t80) cc_final: 0.9027 (t80) REVERT: D 75 TYR cc_start: 0.8873 (m-80) cc_final: 0.7973 (m-80) REVERT: D 103 TYR cc_start: 0.8737 (t80) cc_final: 0.8424 (t80) REVERT: D 124 MET cc_start: 0.7718 (mmm) cc_final: 0.7294 (mmm) REVERT: D 140 ASN cc_start: 0.9494 (m-40) cc_final: 0.9090 (p0) REVERT: E 41 ASP cc_start: 0.7325 (m-30) cc_final: 0.6506 (m-30) REVERT: E 64 MET cc_start: 0.9557 (ptp) cc_final: 0.9325 (ptp) REVERT: E 71 MET cc_start: 0.8517 (mtp) cc_final: 0.7272 (ttp) REVERT: E 88 VAL cc_start: 0.9105 (t) cc_final: 0.8821 (t) REVERT: E 96 MET cc_start: 0.9345 (mmp) cc_final: 0.9085 (mmp) REVERT: F 75 GLU cc_start: 0.9013 (pp20) cc_final: 0.8745 (pp20) REVERT: F 88 MET cc_start: 0.7925 (tmm) cc_final: 0.6992 (tmm) REVERT: H 10 MET cc_start: 0.9509 (tmm) cc_final: 0.9182 (ppp) REVERT: H 27 MET cc_start: 0.8784 (pmm) cc_final: 0.8545 (pmm) REVERT: H 107 SER cc_start: 0.9496 (m) cc_final: 0.9057 (p) REVERT: H 113 ASP cc_start: 0.9186 (p0) cc_final: 0.8873 (p0) REVERT: L 38 TYR cc_start: 0.9415 (p90) cc_final: 0.8781 (p90) REVERT: L 73 ASN cc_start: 0.9368 (m-40) cc_final: 0.9059 (p0) REVERT: L 93 VAL cc_start: 0.8796 (t) cc_final: 0.8508 (p) REVERT: L 112 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8623 (mp10) REVERT: O 65 LYS cc_start: 0.9662 (mtpt) cc_final: 0.9375 (ttmt) REVERT: P 17 TYR cc_start: 0.8522 (m-80) cc_final: 0.7876 (m-80) REVERT: P 18 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8534 (mp10) REVERT: P 34 GLU cc_start: 0.9010 (pp20) cc_final: 0.8750 (pp20) REVERT: Q 11 ARG cc_start: 0.9359 (ppt170) cc_final: 0.9146 (ttp80) REVERT: Q 15 ASP cc_start: 0.8693 (p0) cc_final: 0.8457 (p0) REVERT: Q 17 MET cc_start: 0.8841 (mpp) cc_final: 0.8459 (mpp) REVERT: Q 25 ILE cc_start: 0.9085 (mp) cc_final: 0.8758 (mp) REVERT: Q 27 ARG cc_start: 0.8959 (ptt-90) cc_final: 0.8621 (ptt-90) REVERT: R 29 LEU cc_start: 0.9347 (mm) cc_final: 0.9122 (mm) REVERT: T 13 GLN cc_start: 0.9129 (pp30) cc_final: 0.8906 (pp30) REVERT: T 27 MET cc_start: 0.9174 (tmm) cc_final: 0.8964 (tmm) REVERT: T 54 MET cc_start: 0.9028 (tmm) cc_final: 0.8773 (tmm) REVERT: T 79 LEU cc_start: 0.9330 (mt) cc_final: 0.9102 (mt) REVERT: V 97 PHE cc_start: 0.8943 (m-80) cc_final: 0.8611 (m-10) REVERT: X 91 TYR cc_start: 0.9580 (m-80) cc_final: 0.9104 (m-80) REVERT: X 109 ASN cc_start: 0.8715 (p0) cc_final: 0.8453 (p0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2133 time to fit residues: 95.6962 Evaluate side-chains 227 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: [4, 164, 70, 40, 5, 146, 153, 204, 246, 156, 140] chunk 4 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 54 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.025179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.020809 restraints weight = 505599.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.021589 restraints weight = 211784.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.022074 restraints weight = 120558.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.022379 restraints weight = 82020.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.022579 restraints weight = 63053.871| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37176 Z= 0.258 Angle : 1.075 12.990 55425 Z= 0.437 Chirality : 0.075 0.760 7058 Planarity : 0.005 0.048 3112 Dihedral : 19.789 179.564 14314 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.21), residues: 1458 helix: -0.20 (0.21), residues: 562 sheet: -1.38 (0.29), residues: 291 loop : -1.31 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 20 TYR 0.028 0.002 TYR D 4 PHE 0.020 0.002 PHE F 8 TRP 0.014 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.26 (37175) covalent geometry : angle 1.07468 / 0.44 (55425) hydrogen bonds : bond 0.11815 / 6.18 ( 1203) hydrogen bonds : angle 5.05783 / 2.02 ( 2323) Misc. bond : bond 0.00101 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4940.97 seconds wall clock time: 87 minutes 19.96 seconds (5239.96 seconds total)