Starting phenix.real_space_refine on Sat Mar 7 10:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nqb_0482/03_2026/6nqb_0482.map" } resolution = 3.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1341 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 21496 2.51 5 N 7902 2.21 5 O 11781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42570 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 91} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "A" Number of atoms: 28767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 28767 Classifications: {'RNA': 1341} Modifications used: {'rna2p_pur': 98, 'rna2p_pyr': 68, 'rna3p_pur': 663, 'rna3p_pyr': 512} Link IDs: {'rna2p': 165, 'rna3p': 1175} Chain breaks: 2 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: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 630 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain breaks: 1 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: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "O" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} Chain: "P" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 629 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain breaks: 1 Chain: "T" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 659 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1696 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.38, per 1000 atoms: 0.20 Number of scatterers: 42570 At special positions: 0 Unit cell: (204.943, 215.673, 154.512, 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 49 16.00 P 1341 15.00 Mg 1 11.99 O 11781 8.00 N 7902 7.00 C 21496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 764.3 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 18 sheets defined 33.4% alpha, 9.4% beta 250 base pairs and 620 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'C' and resid 27 through 40 removed outlier: 4.580A pdb=" N LEU C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.889A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.760A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.796A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.367A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 21 Processing helix chain 'J' and resid 22 through 27 removed outlier: 4.352A pdb=" N GLU J 27 " --> pdb=" O ALA J 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 18 removed outlier: 4.596A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU N 15 " --> pdb=" O LYS N 11 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 28 removed outlier: 3.536A pdb=" N LYS N 27 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA N 28 " --> pdb=" O GLU N 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 24 through 28' Processing helix chain 'N' and resid 41 through 49 removed outlier: 3.918A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 89 removed outlier: 3.867A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 16 Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.851A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 removed outlier: 4.139A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE S 73 " --> pdb=" O LEU S 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 69 through 73' Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.564A pdb=" N ILE D 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 4.056A pdb=" N VAL D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.738A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.573A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 157 through 164 removed outlier: 3.619A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.609A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 4.051A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 4.159A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.990A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.835A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 17 through 25 removed outlier: 3.588A pdb=" N MET F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.694A pdb=" N GLU F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'H' and resid 6 through 15 removed outlier: 3.745A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.783A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 39 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.409A pdb=" N ALA H 115 " --> pdb=" O ASP H 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.596A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.642A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 42 removed outlier: 3.525A pdb=" N ALA O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.587A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU O 66 " --> pdb=" O ARG O 62 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS O 72 " --> pdb=" O TYR O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 4.107A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY P 64 " --> pdb=" O TRP P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 removed outlier: 4.322A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 30 removed outlier: 3.557A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 51 through 60 removed outlier: 3.958A pdb=" N ARG R 56 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 removed outlier: 3.596A pdb=" N LEU R 64 " --> pdb=" O ALA R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 61 through 64' Processing helix chain 'T' and resid 6 through 41 removed outlier: 3.889A pdb=" N GLN T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN T 20 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 25 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET T 26 " --> pdb=" O SER T 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 60 removed outlier: 3.619A pdb=" N PHE T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.725A pdb=" N ASP T 58 " --> pdb=" O GLN T 54 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 86 removed outlier: 3.904A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 4.320A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.290A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.827A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 removed outlier: 4.019A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.592A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 51 through 55 removed outlier: 3.511A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 68 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'J' and resid 6 through 12 removed outlier: 3.707A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR J 69 " --> pdb=" O ARG J 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 3.747A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'E' and resid 12 through 14 removed outlier: 3.967A pdb=" N THR E 36 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.748A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 23 through 24 removed outlier: 3.988A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 100 through 104 removed outlier: 7.386A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU H 123 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.597A pdb=" N GLY L 31 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 51 through 55 Processing sheet with id=AB6, first strand: chain 'P' and resid 18 through 21 removed outlier: 4.345A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 7 through 10 removed outlier: 4.025A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ARG Q 61 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU Q 74 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR Q 41 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE Q 24 " --> pdb=" O THR Q 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.303A pdb=" N GLY B 32 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.165A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 594 hydrogen bonds 890 hydrogen bond angles 0 basepair planarities 250 basepair parallelities 620 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5140 1.32 - 1.45: 19614 1.45 - 1.57: 18690 1.57 - 1.69: 2681 1.69 - 1.81: 88 Bond restraints: 46213 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.30e-02 5.92e+03 1.33e+01 bond pdb=" CA ARG R 62 " pdb=" C ARG R 62 " ideal model delta sigma weight residual 1.522 1.569 -0.046 1.37e-02 5.33e+03 1.14e+01 bond pdb=" CA THR B 71 " pdb=" C THR B 71 " ideal model delta sigma weight residual 1.518 1.629 -0.111 4.01e-02 6.22e+02 7.62e+00 bond pdb=" C SER H 78 " pdb=" N ARG H 79 " ideal model delta sigma weight residual 1.339 1.202 0.137 5.57e-02 3.22e+02 6.09e+00 bond pdb=" CA TYR C 167 " pdb=" CB TYR C 167 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.62e-02 3.81e+03 3.89e+00 ... (remaining 46208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 68385 3.63 - 7.27: 601 7.27 - 10.90: 55 10.90 - 14.53: 10 14.53 - 18.17: 1 Bond angle restraints: 69052 Sorted by residual: angle pdb=" C THR B 19 " pdb=" N ARG B 20 " pdb=" CA ARG B 20 " ideal model delta sigma weight residual 120.38 130.91 -10.53 1.37e+00 5.33e-01 5.90e+01 angle pdb=" N ARG Q 5 " pdb=" CA ARG Q 5 " pdb=" C ARG Q 5 " ideal model delta sigma weight residual 114.64 105.31 9.33 1.52e+00 4.33e-01 3.77e+01 angle pdb=" N ALA F 66 " pdb=" CA ALA F 66 " pdb=" C ALA F 66 " ideal model delta sigma weight residual 109.60 116.39 -6.79 1.15e+00 7.56e-01 3.48e+01 angle pdb=" N THR F 26 " pdb=" CA THR F 26 " pdb=" C THR F 26 " ideal model delta sigma weight residual 113.38 106.31 7.07 1.23e+00 6.61e-01 3.30e+01 angle pdb=" N ILE H 6 " pdb=" CA ILE H 6 " pdb=" C ILE H 6 " ideal model delta sigma weight residual 112.96 107.35 5.61 1.00e+00 1.00e+00 3.15e+01 ... (remaining 69047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 25844 35.95 - 71.91: 3342 71.91 - 107.86: 419 107.86 - 143.82: 9 143.82 - 179.77: 11 Dihedral angle restraints: 29625 sinusoidal: 24596 harmonic: 5029 Sorted by residual: dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 65.79 134.21 1 1.50e+01 4.44e-03 7.24e+01 dihedral pdb=" O4' U A 85 " pdb=" C1' U A 85 " pdb=" N1 U A 85 " pdb=" C2 U A 85 " ideal model delta sinusoidal sigma weight residual 232.00 52.23 179.77 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A1322 " pdb=" C1' C A1322 " pdb=" N1 C A1322 " pdb=" C2 C A1322 " ideal model delta sinusoidal sigma weight residual -128.00 48.56 -176.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 29622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7983 0.075 - 0.151: 765 0.151 - 0.226: 58 0.226 - 0.301: 9 0.301 - 0.377: 9 Chirality restraints: 8824 Sorted by residual: chirality pdb=" C1' U A 365 " pdb=" O4' U A 365 " pdb=" C2' U A 365 " pdb=" N1 U A 365 " both_signs ideal model delta sigma weight residual False 2.47 2.09 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB ILE Q 54 " pdb=" CA ILE Q 54 " pdb=" CG1 ILE Q 54 " pdb=" CG2 ILE Q 54 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C3' C A 372 " pdb=" C4' C A 372 " pdb=" O3' C A 372 " pdb=" C2' C A 372 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 8821 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 23 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 24 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 24 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 24 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS L 26 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.78e+00 pdb=" N PRO L 27 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO L 27 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 27 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN P 40 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO P 41 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 41 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO P 41 " -0.038 5.00e-02 4.00e+02 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 7047 2.75 - 3.29: 37901 3.29 - 3.83: 89123 3.83 - 4.36: 101178 4.36 - 4.90: 137572 Nonbonded interactions: 372821 Sorted by model distance: nonbonded pdb=" O2' U A 662 " pdb=" OP1 G A 836 " model vdw 2.216 3.040 nonbonded pdb=" O SER N 99 " pdb=" O2' C A1114 " model vdw 2.227 3.040 nonbonded pdb=" O2' U A 343 " pdb=" O6 G A 346 " model vdw 2.239 3.040 nonbonded pdb=" OP2 C A 522 " pdb=" OH TYR L 65 " model vdw 2.260 3.040 nonbonded pdb=" OP1 U A 62 " pdb=" O2' C A 385 " model vdw 2.263 3.040 ... (remaining 372816 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: 2.030 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: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 42.400 Find NCS groups from input model: 0.180 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.006 0.137 46213 Z= 0.292 Angle : 0.981 18.166 69052 Z= 0.501 Chirality : 0.047 0.377 8824 Planarity : 0.006 0.080 3762 Dihedral : 24.158 179.773 26369 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.64 % Favored : 86.31 % Rotamer: Outliers : 0.41 % Allowed : 5.01 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.36 (0.15), residues: 1716 helix: -4.19 (0.12), residues: 487 sheet: -3.39 (0.28), residues: 231 loop : -3.37 (0.16), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 13 TYR 0.029 0.003 TYR L 65 PHE 0.028 0.003 PHE B 49 TRP 0.042 0.003 TRP B 22 HIS 0.020 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00559 (46213) covalent geometry : angle 0.98116 (69052) hydrogen bonds : bond 0.31374 ( 915) hydrogen bonds : angle 12.00358 ( 1793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 542 time to evaluate : 0.794 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: C 32 LEU cc_start: 0.8512 (pt) cc_final: 0.8058 (tp) REVERT: C 36 PHE cc_start: 0.9092 (t80) cc_final: 0.8795 (t80) REVERT: C 42 LEU cc_start: 0.8055 (mt) cc_final: 0.7803 (mt) REVERT: C 108 PRO cc_start: 0.6733 (Cg_endo) cc_final: 0.6221 (Cg_exo) REVERT: C 182 ASP cc_start: 0.7466 (t0) cc_final: 0.6987 (t0) REVERT: C 186 SER cc_start: 0.8401 (t) cc_final: 0.8035 (t) REVERT: J 52 LEU cc_start: 0.9090 (mp) cc_final: 0.8604 (tp) REVERT: J 69 THR cc_start: 0.7293 (m) cc_final: 0.6945 (p) REVERT: J 88 MET cc_start: 0.6361 (mpp) cc_final: 0.6076 (ptp) REVERT: N 57 SER cc_start: 0.7049 (m) cc_final: 0.6169 (t) REVERT: N 81 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7181 (pp) REVERT: N 82 LYS cc_start: 0.8129 (mmpt) cc_final: 0.7751 (mmtm) REVERT: N 83 VAL cc_start: 0.9056 (t) cc_final: 0.8845 (t) REVERT: N 92 ILE cc_start: 0.8438 (mt) cc_final: 0.8115 (pt) REVERT: D 69 ARG cc_start: 0.8708 (mmp-170) cc_final: 0.7764 (ptt180) REVERT: D 147 LYS cc_start: 0.7851 (mttt) cc_final: 0.7563 (mmmt) REVERT: D 195 ASN cc_start: 0.8263 (m-40) cc_final: 0.7839 (t0) REVERT: E 93 VAL cc_start: 0.9586 (t) cc_final: 0.9368 (m) REVERT: E 94 PHE cc_start: 0.8663 (t80) cc_final: 0.8253 (t80) REVERT: F 4 TYR cc_start: 0.5743 (m-80) cc_final: 0.4908 (m-80) REVERT: F 17 GLN cc_start: 0.8004 (tt0) cc_final: 0.7798 (tp40) REVERT: F 68 GLN cc_start: 0.6458 (pm20) cc_final: 0.4736 (mm-40) REVERT: F 89 VAL cc_start: 0.7443 (t) cc_final: 0.6487 (m) REVERT: H 30 LYS cc_start: 0.8473 (mmpt) cc_final: 0.7802 (mttt) REVERT: H 37 ASN cc_start: 0.8116 (t0) cc_final: 0.7108 (t0) REVERT: H 87 ARG cc_start: 0.7385 (ttm170) cc_final: 0.7020 (ttt-90) REVERT: L 63 THR cc_start: 0.6556 (t) cc_final: 0.6126 (t) REVERT: L 69 GLU cc_start: 0.7089 (tt0) cc_final: 0.6315 (mm-30) REVERT: O 16 ARG cc_start: 0.8055 (ptp-170) cc_final: 0.7350 (mtm-85) REVERT: O 38 LEU cc_start: 0.8516 (mt) cc_final: 0.8089 (tt) REVERT: P 5 ARG cc_start: 0.8456 (pmt100) cc_final: 0.8255 (ptt90) REVERT: P 35 ARG cc_start: 0.8844 (tmm160) cc_final: 0.8638 (tmm-80) REVERT: Q 59 GLU cc_start: 0.7849 (mm-30) cc_final: 0.6304 (mm-30) REVERT: T 31 ILE cc_start: 0.9434 (mt) cc_final: 0.9118 (mt) REVERT: T 53 MET cc_start: 0.8431 (ptm) cc_final: 0.8075 (ppp) REVERT: T 56 ILE cc_start: 0.8880 (mt) cc_final: 0.8507 (mm) REVERT: B 29 PHE cc_start: 0.8392 (m-80) cc_final: 0.8012 (m-80) REVERT: B 112 ARG cc_start: 0.4519 (ttt90) cc_final: 0.1826 (ttm110) REVERT: B 136 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6005 (mtm110) REVERT: B 191 ASP cc_start: 0.6505 (t0) cc_final: 0.6286 (t70) outliers start: 6 outliers final: 1 residues processed: 545 average time/residue: 0.3069 time to fit residues: 254.1327 Evaluate side-chains 320 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 HIS C 24 ASN C 175 HIS N 59 GLN D 119 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS F 55 HIS F 63 ASN H 15 ASN H 17 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 38 HIS B 121 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.101317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.076194 restraints weight = 191896.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078344 restraints weight = 71088.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.078776 restraints weight = 38800.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.078859 restraints weight = 30421.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.078992 restraints weight = 30951.240| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 46213 Z= 0.234 Angle : 0.764 15.436 69052 Z= 0.393 Chirality : 0.042 0.304 8824 Planarity : 0.006 0.072 3762 Dihedral : 25.181 179.821 22897 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.94 % Favored : 87.00 % Rotamer: Outliers : 4.12 % Allowed : 15.18 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.51 (0.17), residues: 1716 helix: -2.92 (0.18), residues: 515 sheet: -3.22 (0.30), residues: 231 loop : -3.06 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 91 TYR 0.014 0.002 TYR H 64 PHE 0.024 0.002 PHE D 106 TRP 0.025 0.002 TRP Q 72 HIS 0.009 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00450 (46213) covalent geometry : angle 0.76350 (69052) hydrogen bonds : bond 0.10093 ( 915) hydrogen bonds : angle 5.27379 ( 1793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 0.575 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: C 32 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 36 PHE cc_start: 0.9059 (t80) cc_final: 0.8709 (t80) REVERT: C 111 ASP cc_start: 0.8109 (t70) cc_final: 0.7881 (t70) REVERT: C 143 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6433 (mp) REVERT: C 182 ASP cc_start: 0.7475 (t0) cc_final: 0.7079 (t0) REVERT: J 52 LEU cc_start: 0.9068 (mp) cc_final: 0.8546 (tp) REVERT: N 5 MET cc_start: 0.5979 (tpt) cc_final: 0.5479 (tpp) REVERT: N 27 LYS cc_start: -0.0605 (pptt) cc_final: -0.1391 (ptpt) REVERT: N 57 SER cc_start: 0.7022 (m) cc_final: 0.6618 (t) REVERT: N 75 LYS cc_start: 0.9114 (tptt) cc_final: 0.8893 (tppt) REVERT: N 92 ILE cc_start: 0.8287 (mt) cc_final: 0.7998 (pt) REVERT: S 78 THR cc_start: 0.6852 (m) cc_final: 0.6597 (p) REVERT: D 69 ARG cc_start: 0.8809 (mmp-170) cc_final: 0.7804 (ptt180) REVERT: D 123 MET cc_start: 0.8480 (ttt) cc_final: 0.8108 (ttt) REVERT: D 147 LYS cc_start: 0.7670 (mttt) cc_final: 0.7392 (mmmt) REVERT: D 195 ASN cc_start: 0.8360 (m-40) cc_final: 0.7925 (t0) REVERT: E 47 PHE cc_start: 0.6711 (p90) cc_final: 0.5935 (p90) REVERT: E 67 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8129 (mtm-85) REVERT: E 94 PHE cc_start: 0.8632 (t80) cc_final: 0.8338 (t80) REVERT: F 9 MET cc_start: 0.5911 (mtt) cc_final: 0.5400 (ppp) REVERT: F 14 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8102 (tp-100) REVERT: F 62 MET cc_start: 0.3198 (mmm) cc_final: 0.2475 (mmm) REVERT: F 68 GLN cc_start: 0.6638 (pm20) cc_final: 0.5342 (mm-40) REVERT: H 2 MET cc_start: 0.4874 (tpt) cc_final: 0.4522 (tpt) REVERT: H 9 MET cc_start: 0.8065 (ttp) cc_final: 0.7642 (tmm) REVERT: H 30 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7572 (mttt) REVERT: H 37 ASN cc_start: 0.8389 (t0) cc_final: 0.7834 (t0) REVERT: H 63 LYS cc_start: 0.5985 (tttt) cc_final: 0.5422 (tppt) REVERT: H 87 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6698 (ttt-90) REVERT: L 69 GLU cc_start: 0.7091 (tt0) cc_final: 0.6270 (mm-30) REVERT: O 16 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7059 (ptt-90) REVERT: O 25 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7518 (mt-10) REVERT: O 38 LEU cc_start: 0.8601 (mt) cc_final: 0.8203 (tp) REVERT: O 61 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7884 (tm-30) REVERT: R 51 GLN cc_start: 0.7687 (pm20) cc_final: 0.6771 (tp40) REVERT: R 69 TYR cc_start: 0.2144 (OUTLIER) cc_final: -0.1305 (m-10) REVERT: T 65 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5905 (mt) REVERT: B 26 MET cc_start: 0.3331 (tpp) cc_final: 0.2618 (tpp) REVERT: B 56 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6443 (mp) REVERT: B 125 PHE cc_start: 0.3661 (t80) cc_final: 0.3181 (t80) REVERT: B 153 MET cc_start: 0.5280 (ttm) cc_final: 0.3461 (mtp) REVERT: B 183 PHE cc_start: 0.1736 (m-10) cc_final: 0.1332 (m-10) REVERT: B 196 ASP cc_start: 0.6278 (p0) cc_final: 0.5929 (p0) outliers start: 60 outliers final: 29 residues processed: 400 average time/residue: 0.2660 time to fit residues: 168.4103 Evaluate side-chains 334 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 238 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 138 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 235 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 264 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN O 37 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS B 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.099372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073358 restraints weight = 195620.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.075437 restraints weight = 69281.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.076663 restraints weight = 37906.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.077344 restraints weight = 27206.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.077645 restraints weight = 22903.689| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 46213 Z= 0.316 Angle : 0.835 13.856 69052 Z= 0.424 Chirality : 0.045 0.334 8824 Planarity : 0.006 0.076 3762 Dihedral : 25.283 178.458 22895 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.38 % Favored : 84.56 % Rotamer: Outliers : 5.63 % Allowed : 17.86 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.22 (0.18), residues: 1716 helix: -2.39 (0.19), residues: 538 sheet: -3.17 (0.30), residues: 226 loop : -3.02 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 43 TYR 0.024 0.003 TYR F 4 PHE 0.036 0.003 PHE N 20 TRP 0.028 0.003 TRP Q 72 HIS 0.010 0.002 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00614 (46213) covalent geometry : angle 0.83455 (69052) hydrogen bonds : bond 0.10263 ( 915) hydrogen bonds : angle 5.07321 ( 1793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 320 time to evaluate : 0.724 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: C 36 PHE cc_start: 0.9057 (t80) cc_final: 0.8771 (t80) REVERT: C 111 ASP cc_start: 0.8405 (t70) cc_final: 0.8098 (t70) REVERT: C 141 MET cc_start: 0.8512 (mmm) cc_final: 0.7972 (tpt) REVERT: C 143 LEU cc_start: 0.6963 (tt) cc_final: 0.6322 (mp) REVERT: C 182 ASP cc_start: 0.7242 (t0) cc_final: 0.6769 (t0) REVERT: J 52 LEU cc_start: 0.9073 (mp) cc_final: 0.8402 (tp) REVERT: N 5 MET cc_start: 0.6212 (tpt) cc_final: 0.5528 (tpp) REVERT: N 9 GLU cc_start: 0.8043 (tp30) cc_final: 0.7811 (tp30) REVERT: N 75 LYS cc_start: 0.9073 (tptt) cc_final: 0.8856 (ttmt) REVERT: S 78 THR cc_start: 0.6912 (m) cc_final: 0.6685 (p) REVERT: D 69 ARG cc_start: 0.8915 (mmp-170) cc_final: 0.7704 (ptt180) REVERT: D 74 TYR cc_start: 0.7888 (m-80) cc_final: 0.7480 (m-80) REVERT: D 123 MET cc_start: 0.8447 (ttt) cc_final: 0.8014 (ttt) REVERT: D 147 LYS cc_start: 0.7732 (mttt) cc_final: 0.7427 (mmmt) REVERT: E 18 ASN cc_start: 0.8559 (m110) cc_final: 0.8287 (m-40) REVERT: E 151 MET cc_start: 0.8487 (mmm) cc_final: 0.8259 (tpp) REVERT: F 62 MET cc_start: 0.3069 (mmm) cc_final: 0.2539 (mmm) REVERT: F 68 GLN cc_start: 0.6410 (pm20) cc_final: 0.5377 (mm110) REVERT: F 88 MET cc_start: 0.7801 (mtt) cc_final: 0.7222 (mpp) REVERT: H 9 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7574 (tmm) REVERT: H 15 ASN cc_start: 0.5986 (OUTLIER) cc_final: 0.5520 (t0) REVERT: H 30 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7588 (mttt) REVERT: H 37 ASN cc_start: 0.8290 (t0) cc_final: 0.7700 (t0) REVERT: H 63 LYS cc_start: 0.5916 (tttt) cc_final: 0.5384 (tppt) REVERT: H 64 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6387 (p90) REVERT: H 87 ARG cc_start: 0.7241 (ttm170) cc_final: 0.6918 (ttt-90) REVERT: L 77 SER cc_start: 0.8139 (m) cc_final: 0.7885 (t) REVERT: O 25 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7736 (mt-10) REVERT: O 38 LEU cc_start: 0.8669 (mt) cc_final: 0.8312 (tp) REVERT: Q 8 GLN cc_start: 0.8252 (tp40) cc_final: 0.8002 (mm-40) REVERT: R 51 GLN cc_start: 0.7766 (pm20) cc_final: 0.6661 (tp-100) REVERT: R 69 TYR cc_start: 0.1751 (OUTLIER) cc_final: -0.1846 (m-80) REVERT: B 44 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8662 (mmmm) REVERT: B 56 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6493 (mp) REVERT: B 183 PHE cc_start: 0.1183 (m-10) cc_final: 0.0676 (m-10) REVERT: B 196 ASP cc_start: 0.6163 (p0) cc_final: 0.5921 (p0) outliers start: 82 outliers final: 45 residues processed: 367 average time/residue: 0.2545 time to fit residues: 150.1624 Evaluate side-chains 320 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 229 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 68 optimal weight: 7.9990 chunk 192 optimal weight: 0.0570 chunk 251 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 166 optimal weight: 50.0000 chunk 275 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS P 26 ASN ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 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 = 0.4158 r_free = 0.4158 target = 0.101789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076223 restraints weight = 191429.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.078364 restraints weight = 66706.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.079614 restraints weight = 35869.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080350 restraints weight = 25436.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.080661 restraints weight = 21187.540| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 46213 Z= 0.192 Angle : 0.681 12.901 69052 Z= 0.352 Chirality : 0.039 0.284 8824 Planarity : 0.005 0.069 3762 Dihedral : 24.960 177.795 22895 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.82 % Favored : 87.12 % Rotamer: Outliers : 4.46 % Allowed : 20.67 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.70 (0.19), residues: 1716 helix: -1.85 (0.21), residues: 532 sheet: -2.73 (0.31), residues: 249 loop : -2.80 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 64 TYR 0.017 0.002 TYR C 167 PHE 0.021 0.002 PHE D 106 TRP 0.019 0.002 TRP C 166 HIS 0.025 0.002 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00373 (46213) covalent geometry : angle 0.68075 (69052) hydrogen bonds : bond 0.08812 ( 915) hydrogen bonds : angle 4.52696 ( 1793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 0.845 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: C 36 PHE cc_start: 0.9029 (t80) cc_final: 0.8767 (t80) REVERT: C 111 ASP cc_start: 0.8569 (t70) cc_final: 0.8205 (t70) REVERT: C 143 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6708 (tt) REVERT: C 182 ASP cc_start: 0.7487 (t0) cc_final: 0.6994 (t0) REVERT: J 52 LEU cc_start: 0.9008 (mp) cc_final: 0.8402 (tp) REVERT: N 5 MET cc_start: 0.6259 (tpt) cc_final: 0.5716 (tpp) REVERT: N 9 GLU cc_start: 0.7989 (tp30) cc_final: 0.7747 (tp30) REVERT: N 92 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8271 (pt) REVERT: S 78 THR cc_start: 0.6918 (m) cc_final: 0.6645 (p) REVERT: D 69 ARG cc_start: 0.8889 (mmp-170) cc_final: 0.7654 (ptt180) REVERT: D 123 MET cc_start: 0.8408 (ttt) cc_final: 0.7899 (mtp) REVERT: D 147 LYS cc_start: 0.7674 (mttt) cc_final: 0.7383 (mmmt) REVERT: D 194 ILE cc_start: 0.8372 (mp) cc_final: 0.8140 (mm) REVERT: E 18 ASN cc_start: 0.8442 (m110) cc_final: 0.8083 (m-40) REVERT: E 67 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8233 (ttm110) REVERT: F 24 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7798 (mtm110) REVERT: F 62 MET cc_start: 0.2987 (mmm) cc_final: 0.2527 (mmm) REVERT: F 68 GLN cc_start: 0.6597 (pm20) cc_final: 0.5682 (mm-40) REVERT: F 88 MET cc_start: 0.7791 (mtt) cc_final: 0.7304 (mpp) REVERT: H 9 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7604 (tmm) REVERT: H 15 ASN cc_start: 0.6003 (OUTLIER) cc_final: 0.5395 (t0) REVERT: H 30 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7779 (ttpt) REVERT: H 37 ASN cc_start: 0.8322 (t0) cc_final: 0.8087 (t0) REVERT: H 63 LYS cc_start: 0.5959 (tttt) cc_final: 0.5427 (tppt) REVERT: H 64 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.5913 (p90) REVERT: H 87 ARG cc_start: 0.7091 (ttm170) cc_final: 0.6784 (ttt-90) REVERT: O 25 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7829 (mt-10) REVERT: O 38 LEU cc_start: 0.8632 (mt) cc_final: 0.8386 (tp) REVERT: O 42 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7945 (t80) REVERT: Q 8 GLN cc_start: 0.8151 (tp40) cc_final: 0.7842 (mm-40) REVERT: R 51 GLN cc_start: 0.7711 (pm20) cc_final: 0.6743 (tp-100) REVERT: R 69 TYR cc_start: 0.1622 (OUTLIER) cc_final: -0.1878 (m-10) REVERT: T 26 MET cc_start: 0.8875 (ttp) cc_final: 0.8654 (tmm) REVERT: T 53 MET cc_start: 0.8627 (ttp) cc_final: 0.8390 (ttp) REVERT: B 44 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8555 (mmmm) REVERT: B 183 PHE cc_start: 0.1344 (m-10) cc_final: 0.0842 (m-10) outliers start: 65 outliers final: 37 residues processed: 356 average time/residue: 0.2591 time to fit residues: 149.0771 Evaluate side-chains 328 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 256 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 167 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 164 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 ASN L 5 GLN O 37 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN ** T 60 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 = 0.4131 r_free = 0.4131 target = 0.100308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.074481 restraints weight = 193666.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.076585 restraints weight = 68111.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.077818 restraints weight = 37001.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078516 restraints weight = 26441.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.078876 restraints weight = 22144.360| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 46213 Z= 0.277 Angle : 0.755 12.464 69052 Z= 0.385 Chirality : 0.042 0.305 8824 Planarity : 0.005 0.076 3762 Dihedral : 25.001 178.065 22895 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.80 % Favored : 85.14 % Rotamer: Outliers : 5.70 % Allowed : 21.50 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.66 (0.19), residues: 1716 helix: -1.86 (0.21), residues: 532 sheet: -2.67 (0.32), residues: 242 loop : -2.76 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 13 TYR 0.014 0.002 TYR F 4 PHE 0.030 0.002 PHE F 78 TRP 0.026 0.002 TRP C 166 HIS 0.009 0.002 HIS O 41 Details of bonding type rmsd covalent geometry : bond 0.00537 (46213) covalent geometry : angle 0.75548 (69052) hydrogen bonds : bond 0.09233 ( 915) hydrogen bonds : angle 4.67783 ( 1793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 293 time to evaluate : 0.889 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: C 36 PHE cc_start: 0.9026 (t80) cc_final: 0.8817 (t80) REVERT: C 130 ARG cc_start: 0.6787 (tmm-80) cc_final: 0.5684 (tmt170) REVERT: C 141 MET cc_start: 0.8414 (mmm) cc_final: 0.7830 (tpt) REVERT: C 169 GLU cc_start: 0.7495 (tp30) cc_final: 0.6883 (mp0) REVERT: C 183 TYR cc_start: 0.8287 (t80) cc_final: 0.8000 (t80) REVERT: J 52 LEU cc_start: 0.8996 (mp) cc_final: 0.8401 (tp) REVERT: N 5 MET cc_start: 0.6298 (tpt) cc_final: 0.6009 (tpp) REVERT: N 19 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: N 92 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8225 (pt) REVERT: S 28 LYS cc_start: 0.5066 (OUTLIER) cc_final: 0.4816 (pmmt) REVERT: S 78 THR cc_start: 0.6969 (m) cc_final: 0.6687 (p) REVERT: D 123 MET cc_start: 0.8455 (ttt) cc_final: 0.8030 (ttt) REVERT: D 147 LYS cc_start: 0.7733 (mttt) cc_final: 0.7435 (mmmt) REVERT: D 194 ILE cc_start: 0.8327 (mp) cc_final: 0.8108 (mm) REVERT: E 18 ASN cc_start: 0.8493 (m110) cc_final: 0.8118 (m-40) REVERT: E 67 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8272 (ttm110) REVERT: F 24 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7706 (mtm110) REVERT: F 62 MET cc_start: 0.2917 (mmm) cc_final: 0.2306 (mmm) REVERT: F 68 GLN cc_start: 0.6856 (pm20) cc_final: 0.5803 (mm-40) REVERT: F 88 MET cc_start: 0.7841 (mtt) cc_final: 0.7333 (mpp) REVERT: H 9 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7627 (tmm) REVERT: H 15 ASN cc_start: 0.6094 (OUTLIER) cc_final: 0.5474 (t0) REVERT: H 37 ASN cc_start: 0.8261 (t0) cc_final: 0.7792 (t0) REVERT: H 63 LYS cc_start: 0.6188 (tttt) cc_final: 0.5398 (tppt) REVERT: H 64 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6259 (p90) REVERT: H 87 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6854 (ttt-90) REVERT: L 75 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: O 25 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7865 (mt-10) REVERT: O 38 LEU cc_start: 0.8614 (mt) cc_final: 0.8200 (tp) REVERT: O 42 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7991 (t80) REVERT: O 53 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6860 (ttm170) REVERT: O 58 MET cc_start: 0.8336 (ptp) cc_final: 0.8065 (ptp) REVERT: Q 14 ASP cc_start: 0.8425 (t0) cc_final: 0.7969 (p0) REVERT: R 51 GLN cc_start: 0.7736 (pm20) cc_final: 0.6714 (tp-100) REVERT: R 69 TYR cc_start: 0.1819 (OUTLIER) cc_final: -0.1828 (m-10) REVERT: T 26 MET cc_start: 0.8936 (ttp) cc_final: 0.8693 (tmm) REVERT: B 44 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8531 (mmmm) REVERT: B 196 ASP cc_start: 0.6281 (p0) cc_final: 0.6022 (p0) outliers start: 83 outliers final: 54 residues processed: 342 average time/residue: 0.2513 time to fit residues: 139.1482 Evaluate side-chains 340 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 91 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 194 optimal weight: 0.5980 chunk 123 optimal weight: 20.0000 chunk 292 optimal weight: 7.9990 chunk 221 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 268 optimal weight: 0.0970 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN O 37 HIS ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 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 = 0.4170 r_free = 0.4170 target = 0.102409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.076744 restraints weight = 192751.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.078917 restraints weight = 67491.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.080211 restraints weight = 36363.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080931 restraints weight = 25769.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.081276 restraints weight = 21499.933| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 46213 Z= 0.175 Angle : 0.652 12.219 69052 Z= 0.336 Chirality : 0.038 0.317 8824 Planarity : 0.005 0.066 3762 Dihedral : 24.791 177.555 22895 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.18 % Favored : 87.76 % Rotamer: Outliers : 5.22 % Allowed : 23.08 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.31 (0.19), residues: 1716 helix: -1.46 (0.22), residues: 523 sheet: -2.52 (0.32), residues: 252 loop : -2.60 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 164 TYR 0.016 0.002 TYR F 25 PHE 0.032 0.002 PHE B 89 TRP 0.028 0.002 TRP C 166 HIS 0.043 0.002 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00337 (46213) covalent geometry : angle 0.65181 (69052) hydrogen bonds : bond 0.08542 ( 915) hydrogen bonds : angle 4.34227 ( 1793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 302 time to evaluate : 0.831 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: C 36 PHE cc_start: 0.9022 (t80) cc_final: 0.8779 (t80) REVERT: C 130 ARG cc_start: 0.7070 (tmm-80) cc_final: 0.6012 (tmt170) REVERT: C 141 MET cc_start: 0.8264 (mmm) cc_final: 0.7856 (tpt) REVERT: J 52 LEU cc_start: 0.8967 (mp) cc_final: 0.8340 (tp) REVERT: N 5 MET cc_start: 0.6215 (tpt) cc_final: 0.5760 (tpp) REVERT: N 19 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: S 28 LYS cc_start: 0.5061 (OUTLIER) cc_final: 0.4796 (pmmt) REVERT: S 78 THR cc_start: 0.7061 (m) cc_final: 0.6776 (p) REVERT: D 147 LYS cc_start: 0.7749 (mttt) cc_final: 0.7453 (mmmt) REVERT: D 194 ILE cc_start: 0.8281 (mp) cc_final: 0.8048 (mm) REVERT: E 67 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8241 (ttm110) REVERT: E 68 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7844 (mmp80) REVERT: F 24 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7616 (mtm110) REVERT: F 62 MET cc_start: 0.2927 (mmm) cc_final: 0.2362 (mmm) REVERT: F 68 GLN cc_start: 0.6743 (pm20) cc_final: 0.5854 (mm-40) REVERT: F 88 MET cc_start: 0.7783 (mtt) cc_final: 0.7296 (mpp) REVERT: H 15 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.5387 (t0) REVERT: H 37 ASN cc_start: 0.8282 (t0) cc_final: 0.8072 (t0) REVERT: H 63 LYS cc_start: 0.5931 (tttt) cc_final: 0.5307 (tppt) REVERT: H 64 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.5918 (p90) REVERT: H 87 ARG cc_start: 0.6915 (ttm170) cc_final: 0.6570 (ttt-90) REVERT: O 25 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7793 (mt-10) REVERT: O 38 LEU cc_start: 0.8583 (mt) cc_final: 0.8128 (tt) REVERT: O 42 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7998 (t80) REVERT: O 53 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6650 (ttm170) REVERT: O 58 MET cc_start: 0.8284 (ptp) cc_final: 0.8072 (ptp) REVERT: R 51 GLN cc_start: 0.7719 (pm20) cc_final: 0.6724 (tp-100) REVERT: R 69 TYR cc_start: 0.1871 (OUTLIER) cc_final: -0.1636 (m-10) REVERT: B 44 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8518 (mmmm) REVERT: B 196 ASP cc_start: 0.6276 (p0) cc_final: 0.6060 (p0) outliers start: 76 outliers final: 50 residues processed: 350 average time/residue: 0.2621 time to fit residues: 148.0282 Evaluate side-chains 332 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 236 optimal weight: 0.8980 chunk 167 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 258 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 154 optimal weight: 40.0000 chunk 283 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 60 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 = 0.4170 r_free = 0.4170 target = 0.101938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077678 restraints weight = 195838.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.079750 restraints weight = 84013.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079951 restraints weight = 40955.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079956 restraints weight = 34976.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.080120 restraints weight = 34428.397| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 46213 Z= 0.232 Angle : 0.702 15.211 69052 Z= 0.360 Chirality : 0.039 0.340 8824 Planarity : 0.005 0.093 3762 Dihedral : 24.818 177.341 22895 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.75 % Favored : 86.19 % Rotamer: Outliers : 5.98 % Allowed : 22.94 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.30 (0.19), residues: 1716 helix: -1.44 (0.22), residues: 526 sheet: -2.54 (0.31), residues: 251 loop : -2.59 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 28 TYR 0.015 0.002 TYR L 37 PHE 0.027 0.002 PHE B 89 TRP 0.030 0.002 TRP C 166 HIS 0.008 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00451 (46213) covalent geometry : angle 0.70205 (69052) hydrogen bonds : bond 0.08779 ( 915) hydrogen bonds : angle 4.46379 ( 1793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 0.617 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: C 36 PHE cc_start: 0.9027 (t80) cc_final: 0.8821 (t80) REVERT: C 130 ARG cc_start: 0.7077 (tmm-80) cc_final: 0.5982 (tmt170) REVERT: C 141 MET cc_start: 0.8231 (mmm) cc_final: 0.7741 (tpt) REVERT: J 52 LEU cc_start: 0.8961 (mp) cc_final: 0.8547 (tp) REVERT: N 19 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: S 28 LYS cc_start: 0.4795 (OUTLIER) cc_final: 0.4495 (pmmt) REVERT: S 78 THR cc_start: 0.7199 (m) cc_final: 0.6860 (p) REVERT: D 3 TYR cc_start: 0.7971 (t80) cc_final: 0.7629 (t80) REVERT: D 46 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6233 (ptt90) REVERT: D 123 MET cc_start: 0.8380 (tpp) cc_final: 0.8018 (tpp) REVERT: D 194 ILE cc_start: 0.8300 (mp) cc_final: 0.8078 (mm) REVERT: E 67 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8382 (tpp80) REVERT: E 140 ILE cc_start: 0.8300 (mt) cc_final: 0.8001 (tp) REVERT: E 144 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7331 (mm-30) REVERT: F 62 MET cc_start: 0.3008 (mmm) cc_final: 0.2429 (mmm) REVERT: F 68 GLN cc_start: 0.6979 (pm20) cc_final: 0.6061 (mm-40) REVERT: F 88 MET cc_start: 0.7853 (mtt) cc_final: 0.7334 (mpp) REVERT: H 15 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5520 (t0) REVERT: H 37 ASN cc_start: 0.8201 (t0) cc_final: 0.7952 (t0) REVERT: H 63 LYS cc_start: 0.6108 (tttt) cc_final: 0.5256 (tppt) REVERT: H 64 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6150 (p90) REVERT: H 87 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6795 (ttt-90) REVERT: O 25 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7744 (mt-10) REVERT: O 42 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8011 (t80) REVERT: O 58 MET cc_start: 0.8161 (ptp) cc_final: 0.7915 (ptp) REVERT: P 28 ARG cc_start: 0.7565 (mmp80) cc_final: 0.7350 (mpp-170) REVERT: R 51 GLN cc_start: 0.7749 (pm20) cc_final: 0.6737 (tp-100) REVERT: R 69 TYR cc_start: 0.1899 (OUTLIER) cc_final: -0.1574 (m-10) REVERT: B 44 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8650 (mmmm) REVERT: B 196 ASP cc_start: 0.6434 (p0) cc_final: 0.6205 (p0) outliers start: 87 outliers final: 59 residues processed: 326 average time/residue: 0.2482 time to fit residues: 132.2077 Evaluate side-chains 336 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 69 TYR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 19 HIS Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 288 optimal weight: 8.9990 chunk 295 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 217 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS ** T 60 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 = 0.4159 r_free = 0.4159 target = 0.101350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.076864 restraints weight = 196527.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.079345 restraints weight = 77162.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079151 restraints weight = 41491.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.079127 restraints weight = 34092.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.079385 restraints weight = 36052.322| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 46213 Z= 0.254 Angle : 0.730 14.975 69052 Z= 0.372 Chirality : 0.041 0.345 8824 Planarity : 0.005 0.089 3762 Dihedral : 24.846 177.914 22895 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.34 % Favored : 85.61 % Rotamer: Outliers : 5.63 % Allowed : 23.35 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -3.31 (0.19), residues: 1716 helix: -1.48 (0.22), residues: 522 sheet: -2.57 (0.31), residues: 253 loop : -2.56 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.012 0.002 TYR L 65 PHE 0.026 0.002 PHE B 15 TRP 0.036 0.002 TRP C 166 HIS 0.008 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00494 (46213) covalent geometry : angle 0.73002 (69052) hydrogen bonds : bond 0.08924 ( 915) hydrogen bonds : angle 4.56004 ( 1793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 275 time to evaluate : 1.012 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: C 36 PHE cc_start: 0.9035 (t80) cc_final: 0.8823 (t80) REVERT: C 130 ARG cc_start: 0.7105 (tmm-80) cc_final: 0.5987 (tmt170) REVERT: C 141 MET cc_start: 0.8000 (mmm) cc_final: 0.7727 (tpt) REVERT: J 52 LEU cc_start: 0.9038 (mp) cc_final: 0.8617 (tp) REVERT: N 5 MET cc_start: 0.6199 (tpp) cc_final: 0.5837 (tpp) REVERT: N 19 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: S 28 LYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4517 (pmmt) REVERT: S 65 MET cc_start: -0.1172 (mtt) cc_final: -0.1476 (mtt) REVERT: S 78 THR cc_start: 0.7116 (m) cc_final: 0.6772 (p) REVERT: D 3 TYR cc_start: 0.7998 (t80) cc_final: 0.7791 (t80) REVERT: D 46 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6251 (ptt90) REVERT: D 123 MET cc_start: 0.8392 (tpp) cc_final: 0.8155 (tpp) REVERT: D 194 ILE cc_start: 0.8319 (mp) cc_final: 0.8104 (mm) REVERT: F 62 MET cc_start: 0.3006 (mmm) cc_final: 0.2421 (mmm) REVERT: F 68 GLN cc_start: 0.7002 (pm20) cc_final: 0.5982 (mm110) REVERT: F 88 MET cc_start: 0.7879 (mtt) cc_final: 0.7380 (mpp) REVERT: H 15 ASN cc_start: 0.6143 (OUTLIER) cc_final: 0.5555 (t0) REVERT: H 37 ASN cc_start: 0.8223 (t0) cc_final: 0.7931 (t0) REVERT: H 63 LYS cc_start: 0.6099 (tttt) cc_final: 0.5241 (tppt) REVERT: H 64 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6234 (p90) REVERT: H 87 ARG cc_start: 0.7110 (ttm170) cc_final: 0.6803 (ttt-90) REVERT: O 3 SER cc_start: 0.8247 (m) cc_final: 0.7714 (p) REVERT: O 25 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7757 (mt-10) REVERT: O 53 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6683 (ttm170) REVERT: O 58 MET cc_start: 0.8173 (ptp) cc_final: 0.7931 (ptp) REVERT: R 51 GLN cc_start: 0.7749 (pm20) cc_final: 0.6692 (tp-100) REVERT: B 26 MET cc_start: 0.2441 (tmm) cc_final: 0.1766 (ttp) REVERT: B 44 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8768 (mmmm) REVERT: B 114 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7324 (mmmt) REVERT: B 196 ASP cc_start: 0.6325 (p0) cc_final: 0.6075 (p0) outliers start: 82 outliers final: 63 residues processed: 322 average time/residue: 0.2438 time to fit residues: 128.3412 Evaluate side-chains 332 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 263 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 126 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 236 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.101789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.077394 restraints weight = 196691.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.079768 restraints weight = 82023.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.079652 restraints weight = 39441.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079870 restraints weight = 35536.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079923 restraints weight = 33540.186| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 46213 Z= 0.220 Angle : 0.708 13.096 69052 Z= 0.363 Chirality : 0.040 0.338 8824 Planarity : 0.005 0.079 3762 Dihedral : 24.828 178.697 22895 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.99 % Favored : 85.96 % Rotamer: Outliers : 5.36 % Allowed : 23.76 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.21 (0.19), residues: 1716 helix: -1.34 (0.22), residues: 518 sheet: -2.57 (0.31), residues: 254 loop : -2.51 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 91 TYR 0.024 0.002 TYR F 25 PHE 0.025 0.002 PHE B 15 TRP 0.046 0.002 TRP C 166 HIS 0.008 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00428 (46213) covalent geometry : angle 0.70831 (69052) hydrogen bonds : bond 0.08814 ( 915) hydrogen bonds : angle 4.46559 ( 1793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 272 time to evaluate : 0.862 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: C 36 PHE cc_start: 0.8979 (t80) cc_final: 0.8725 (t80) REVERT: C 130 ARG cc_start: 0.7118 (tmm-80) cc_final: 0.6002 (tmt170) REVERT: J 42 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7080 (mt) REVERT: J 52 LEU cc_start: 0.8933 (mp) cc_final: 0.8485 (tp) REVERT: N 5 MET cc_start: 0.6220 (tpp) cc_final: 0.5839 (tpp) REVERT: N 19 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7671 (m-10) REVERT: N 91 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7428 (mt-10) REVERT: S 28 LYS cc_start: 0.4744 (OUTLIER) cc_final: 0.4435 (pmmt) REVERT: S 65 MET cc_start: -0.1146 (mtt) cc_final: -0.1465 (mtt) REVERT: S 78 THR cc_start: 0.6751 (m) cc_final: 0.6444 (t) REVERT: D 3 TYR cc_start: 0.7923 (t80) cc_final: 0.7722 (t80) REVERT: D 194 ILE cc_start: 0.8359 (mp) cc_final: 0.8153 (mm) REVERT: F 62 MET cc_start: 0.2972 (mmm) cc_final: 0.2413 (mmm) REVERT: F 68 GLN cc_start: 0.7001 (pm20) cc_final: 0.6161 (mt0) REVERT: H 15 ASN cc_start: 0.6114 (OUTLIER) cc_final: 0.5507 (t0) REVERT: H 37 ASN cc_start: 0.8232 (t0) cc_final: 0.7935 (t0) REVERT: H 63 LYS cc_start: 0.5933 (tttt) cc_final: 0.5228 (tppt) REVERT: H 64 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5856 (p90) REVERT: H 87 ARG cc_start: 0.6990 (ttm170) cc_final: 0.6622 (ttt-90) REVERT: H 90 GLU cc_start: 0.7536 (tt0) cc_final: 0.7329 (tt0) REVERT: O 3 SER cc_start: 0.8500 (m) cc_final: 0.7999 (p) REVERT: O 25 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7764 (mt-10) REVERT: R 51 GLN cc_start: 0.7747 (pm20) cc_final: 0.6668 (tp-100) REVERT: B 26 MET cc_start: 0.2068 (tmm) cc_final: 0.1558 (ttp) REVERT: B 44 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8758 (mmmm) REVERT: B 183 PHE cc_start: 0.2879 (m-80) cc_final: 0.2609 (m-80) REVERT: B 196 ASP cc_start: 0.6387 (p0) cc_final: 0.6162 (p0) outliers start: 78 outliers final: 61 residues processed: 320 average time/residue: 0.2625 time to fit residues: 137.0026 Evaluate side-chains 336 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 241 optimal weight: 6.9990 chunk 138 optimal weight: 40.0000 chunk 167 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS R 73 HIS ** T 60 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 = 0.4141 r_free = 0.4141 target = 0.100397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.076287 restraints weight = 195715.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.078231 restraints weight = 82781.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.078327 restraints weight = 39621.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078150 restraints weight = 36089.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078341 restraints weight = 36282.317| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 46213 Z= 0.312 Angle : 0.799 14.254 69052 Z= 0.405 Chirality : 0.043 0.355 8824 Planarity : 0.006 0.087 3762 Dihedral : 24.910 179.771 22895 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.27 % Favored : 84.67 % Rotamer: Outliers : 4.81 % Allowed : 24.52 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.44 (0.19), residues: 1716 helix: -1.61 (0.22), residues: 528 sheet: -2.75 (0.31), residues: 256 loop : -2.58 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 24 TYR 0.040 0.003 TYR C 167 PHE 0.031 0.003 PHE H 65 TRP 0.050 0.003 TRP C 166 HIS 0.010 0.002 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00605 (46213) covalent geometry : angle 0.79882 (69052) hydrogen bonds : bond 0.09403 ( 915) hydrogen bonds : angle 4.72884 ( 1793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 0.849 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: C 36 PHE cc_start: 0.8986 (t80) cc_final: 0.8761 (t80) REVERT: C 130 ARG cc_start: 0.7150 (tmm-80) cc_final: 0.6236 (tmt170) REVERT: J 52 LEU cc_start: 0.9003 (mp) cc_final: 0.8593 (tp) REVERT: N 5 MET cc_start: 0.6291 (tpp) cc_final: 0.5927 (tpp) REVERT: N 19 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: N 91 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7670 (mt-10) REVERT: S 28 LYS cc_start: 0.4776 (OUTLIER) cc_final: 0.4464 (pmmt) REVERT: S 65 MET cc_start: -0.1345 (mtt) cc_final: -0.1659 (mtt) REVERT: S 78 THR cc_start: 0.6833 (m) cc_final: 0.6494 (t) REVERT: D 194 ILE cc_start: 0.8329 (mp) cc_final: 0.8094 (mm) REVERT: F 62 MET cc_start: 0.3028 (mmm) cc_final: 0.2462 (mmm) REVERT: F 68 GLN cc_start: 0.7118 (pm20) cc_final: 0.6085 (mm110) REVERT: F 73 GLU cc_start: 0.9276 (pm20) cc_final: 0.9028 (pm20) REVERT: H 15 ASN cc_start: 0.6229 (OUTLIER) cc_final: 0.5660 (t0) REVERT: H 37 ASN cc_start: 0.8219 (t0) cc_final: 0.7964 (t0) REVERT: H 63 LYS cc_start: 0.5897 (tttt) cc_final: 0.5215 (tppt) REVERT: H 64 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6332 (p90) REVERT: H 87 ARG cc_start: 0.7246 (ttm170) cc_final: 0.6939 (ttt-90) REVERT: O 3 SER cc_start: 0.8529 (m) cc_final: 0.8034 (p) REVERT: O 25 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7731 (mt-10) REVERT: O 58 MET cc_start: 0.8187 (ptp) cc_final: 0.7897 (pmm) REVERT: Q 16 MET cc_start: 0.6870 (mmt) cc_final: 0.6667 (mmm) REVERT: B 26 MET cc_start: 0.2191 (tmm) cc_final: 0.1857 (ttp) REVERT: B 44 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8754 (mmmm) REVERT: B 166 ASP cc_start: 0.6565 (m-30) cc_final: 0.6345 (m-30) REVERT: B 196 ASP cc_start: 0.6398 (p0) cc_final: 0.6173 (p0) REVERT: B 197 PHE cc_start: 0.6410 (m-80) cc_final: 0.6096 (m-10) outliers start: 70 outliers final: 61 residues processed: 318 average time/residue: 0.2526 time to fit residues: 130.2872 Evaluate side-chains 326 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 261 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 175 HIS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 80 PHE Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 64 TYR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 42 ARG Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 72 ARG Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 111 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 129 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.103173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.077938 restraints weight = 195742.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.080393 restraints weight = 83711.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.080201 restraints weight = 38153.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.080277 restraints weight = 36485.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.080603 restraints weight = 33851.607| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46213 Z= 0.189 Angle : 0.685 13.683 69052 Z= 0.352 Chirality : 0.038 0.328 8824 Planarity : 0.005 0.091 3762 Dihedral : 24.745 179.396 22895 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.70 % Favored : 87.24 % Rotamer: Outliers : 4.46 % Allowed : 25.27 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.24 (0.19), residues: 1716 helix: -1.41 (0.22), residues: 536 sheet: -2.47 (0.33), residues: 240 loop : -2.56 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 24 TYR 0.019 0.002 TYR C 167 PHE 0.031 0.002 PHE H 65 TRP 0.056 0.003 TRP C 166 HIS 0.008 0.001 HIS J 15 Details of bonding type rmsd covalent geometry : bond 0.00368 (46213) covalent geometry : angle 0.68514 (69052) hydrogen bonds : bond 0.08730 ( 915) hydrogen bonds : angle 4.46324 ( 1793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7858.24 seconds wall clock time: 136 minutes 37.82 seconds (8197.82 seconds total)