Starting phenix.real_space_refine on Sun Feb 8 09:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c83_16470/02_2026/8c83_16470.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1177 5.49 5 S 33 5.16 5 C 24295 2.51 5 N 8370 2.21 5 O 11928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45803 Number of models: 1 Model: "" Number of chains: 18 Chain: "x" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1509 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 175} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 815 Unresolved non-hydrogen dihedrals: 554 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 18, 'ARG:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 5, 'GLN:plan1': 10, 'PHE:plan': 4, 'HIS:plan': 7, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 358 Chain: "y" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 374 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "2" Number of atoms: 25088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 25088 Classifications: {'RNA': 1177} Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 64, 'rna3p_pur': 553, 'rna3p_pyr': 486} Link IDs: {'rna2p': 137, 'rna3p': 1039} Chain breaks: 6 Chain: "P" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1603 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1626 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 13, 'TRANS': 202} Chain: "S" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "T" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1815 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1473 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 173} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1479 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 175} 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: "X" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1142 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain: "a" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 673 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "d" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "f" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "g" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 472 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 54} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A 21756 " occ=0.55 ... (20 atoms not shown) pdb=" C4 A 21756 " occ=0.55 Time building chain proxies: 9.53, per 1000 atoms: 0.21 Number of scatterers: 45803 At special positions: 0 Unit cell: (164.145, 200.151, 217.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 1177 15.00 O 11928 8.00 N 8370 7.00 C 24295 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: 3.56 Conformation dependent library (CDL) restraints added in 1.2 seconds 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 30 sheets defined 37.4% alpha, 16.1% beta 354 base pairs and 621 stacking pairs defined. Time for finding SS restraints: 6.37 Creating SS restraints... Processing helix chain 'x' and resid 13 through 37 Processing helix chain 'x' and resid 39 through 72 removed outlier: 4.574A pdb=" N LYS x 44 " --> pdb=" O LYS x 40 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU x 45 " --> pdb=" O SER x 41 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER x 48 " --> pdb=" O LYS x 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS x 49 " --> pdb=" O GLU x 45 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS x 56 " --> pdb=" O ASP x 52 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU x 57 " --> pdb=" O LEU x 53 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU x 62 " --> pdb=" O LYS x 58 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 92 Processing helix chain 'x' and resid 121 through 147 removed outlier: 3.628A pdb=" N GLU x 143 " --> pdb=" O GLU x 139 " (cutoff:3.500A) Processing helix chain 'x' and resid 149 through 166 removed outlier: 3.733A pdb=" N MET x 153 " --> pdb=" O ASP x 149 " (cutoff:3.500A) Processing helix chain 'x' and resid 177 through 191 Processing helix chain 'x' and resid 201 through 216 Processing helix chain 'x' and resid 216 through 224 Proline residue: x 222 - end of helix Processing helix chain 'x' and resid 234 through 245 Processing helix chain 'x' and resid 250 through 261 Processing helix chain 'y' and resid 22 through 35 Processing helix chain 'P' and resid 10 through 18 Processing helix chain 'P' and resid 49 through 67 removed outlier: 3.585A pdb=" N ALA P 66 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 71 No H-bonds generated for 'chain 'P' and resid 69 through 71' Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'P' and resid 129 through 137 Processing helix chain 'P' and resid 166 through 186 removed outlier: 3.937A pdb=" N ILE P 170 " --> pdb=" O GLY P 166 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY P 171 " --> pdb=" O LYS P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 203 removed outlier: 3.855A pdb=" N PHE P 203 " --> pdb=" O ASP P 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 48 Processing helix chain 'R' and resid 53 through 59 removed outlier: 3.720A pdb=" N PHE R 57 " --> pdb=" O ILE R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 73 removed outlier: 4.194A pdb=" N ILE R 69 " --> pdb=" O GLU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 135 Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 206 through 220 Processing helix chain 'R' and resid 221 through 223 No H-bonds generated for 'chain 'R' and resid 221 through 223' Processing helix chain 'R' and resid 226 through 230 Processing helix chain 'R' and resid 238 through 243 Processing helix chain 'S' and resid 15 through 19 Processing helix chain 'S' and resid 44 through 50 Processing helix chain 'S' and resid 57 through 66 Processing helix chain 'S' and resid 94 through 96 No H-bonds generated for 'chain 'S' and resid 94 through 96' Processing helix chain 'S' and resid 117 through 121 removed outlier: 3.582A pdb=" N TYR S 121 " --> pdb=" O GLU S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 135 No H-bonds generated for 'chain 'S' and resid 133 through 135' Processing helix chain 'S' and resid 247 through 258 Processing helix chain 'T' and resid 23 through 28 removed outlier: 3.882A pdb=" N VAL T 26 " --> pdb=" O ARG T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 61 No H-bonds generated for 'chain 'T' and resid 59 through 61' Processing helix chain 'T' and resid 137 through 146 Processing helix chain 'T' and resid 152 through 156 removed outlier: 3.539A pdb=" N ASP T 155 " --> pdb=" O ASP T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 226 removed outlier: 3.616A pdb=" N VAL T 195 " --> pdb=" O ARG T 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.541A pdb=" N LEU U 9 " --> pdb=" O GLN U 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 5 through 9' Processing helix chain 'U' and resid 14 through 30 Processing helix chain 'U' and resid 66 through 85 removed outlier: 3.526A pdb=" N PHE U 70 " --> pdb=" O SER U 66 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL U 73 " --> pdb=" O GLY U 69 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 116 Processing helix chain 'U' and resid 117 through 130 removed outlier: 3.761A pdb=" N VAL U 130 " --> pdb=" O LEU U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 164 removed outlier: 3.656A pdb=" N GLN U 161 " --> pdb=" O ASP U 158 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP U 163 " --> pdb=" O GLN U 160 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TYR U 164 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 165 through 178 Processing helix chain 'V' and resid 6 through 10 removed outlier: 4.187A pdb=" N HIS V 9 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS V 10 " --> pdb=" O SER V 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 6 through 10' Processing helix chain 'V' and resid 25 through 27 No H-bonds generated for 'chain 'V' and resid 25 through 27' Processing helix chain 'V' and resid 88 through 93 Processing helix chain 'V' and resid 106 through 117 removed outlier: 3.594A pdb=" N ARG V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 146 Processing helix chain 'V' and resid 153 through 163 removed outlier: 3.531A pdb=" N GLU V 157 " --> pdb=" O GLU V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 186 through 197 Processing helix chain 'W' and resid 20 through 35 Processing helix chain 'W' and resid 39 through 62 removed outlier: 4.204A pdb=" N ARG W 62 " --> pdb=" O ASP W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 84 Processing helix chain 'W' and resid 100 through 106 removed outlier: 3.883A pdb=" N PHE W 104 " --> pdb=" O LYS W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 116 Processing helix chain 'W' and resid 121 through 130 Processing helix chain 'W' and resid 151 through 155 Processing helix chain 'W' and resid 170 through 185 Processing helix chain 'X' and resid 45 through 51 removed outlier: 3.522A pdb=" N ILE X 49 " --> pdb=" O PRO X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 43 removed outlier: 3.542A pdb=" N VAL Y 33 " --> pdb=" O SER Y 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS Y 43 " --> pdb=" O LYS Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 57 Processing helix chain 'Y' and resid 62 through 67 Processing helix chain 'Y' and resid 70 through 78 removed outlier: 3.677A pdb=" N ILE Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 105 Processing helix chain 'Y' and resid 108 through 132 Processing helix chain 'Y' and resid 142 through 150 removed outlier: 4.049A pdb=" N ALA Y 148 " --> pdb=" O ALA Y 144 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL Y 150 " --> pdb=" O ALA Y 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 62 Processing helix chain 'a' and resid 64 through 76 Processing helix chain 'b' and resid 5 through 21 Processing helix chain 'b' and resid 31 through 44 removed outlier: 3.600A pdb=" N ILE b 35 " --> pdb=" O SER b 31 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 removed outlier: 4.108A pdb=" N GLU b 87 " --> pdb=" O ILE b 83 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU b 94 " --> pdb=" O THR b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 120 Processing helix chain 'c' and resid 11 through 24 removed outlier: 3.530A pdb=" N LEU c 15 " --> pdb=" O SER c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 34 Processing helix chain 'c' and resid 35 through 40 Processing helix chain 'c' and resid 91 through 96 removed outlier: 3.689A pdb=" N ASN c 94 " --> pdb=" O GLY c 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL c 96 " --> pdb=" O LEU c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 137 Processing helix chain 'd' and resid 36 through 48 Processing helix chain 'd' and resid 78 through 86 Processing helix chain 'd' and resid 87 through 94 Processing helix chain 'd' and resid 104 through 116 Processing helix chain 'd' and resid 122 through 133 Processing helix chain 'f' and resid 11 through 18 Processing helix chain 'g' and resid 7 through 11 removed outlier: 3.780A pdb=" N ARG g 10 " --> pdb=" O SER g 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 11 " --> pdb=" O LEU g 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 7 through 11' Processing helix chain 'g' and resid 12 through 18 Processing helix chain 'g' and resid 32 through 44 Processing sheet with id=AA1, first strand: chain 'x' and resid 167 through 169 removed outlier: 4.465A pdb=" N LYS x 287 " --> pdb=" O LEU x 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 225 through 226 removed outlier: 3.505A pdb=" N ASP x 226 " --> pdb=" O LYS x 231 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS x 231 " --> pdb=" O ASP x 226 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'y' and resid 12 through 16 Processing sheet with id=AA4, first strand: chain 'P' and resid 96 through 99 removed outlier: 6.139A pdb=" N VAL P 73 " --> pdb=" O THR P 96 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE P 98 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA P 75 " --> pdb=" O ILE P 98 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL P 121 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 77 through 89 removed outlier: 5.687A pdb=" N ASP R 78 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY R 105 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL R 80 " --> pdb=" O VAL R 103 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL R 103 " --> pdb=" O VAL R 80 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN R 82 " --> pdb=" O VAL R 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL R 101 " --> pdb=" O ASN R 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'R' and resid 158 through 162 removed outlier: 3.568A pdb=" N THR R 198 " --> pdb=" O VAL R 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 42 through 43 Processing sheet with id=AA9, first strand: chain 'S' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'S' and resid 102 through 103 removed outlier: 4.276A pdb=" N VAL S 102 " --> pdb=" O ALA S 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 122 through 125 removed outlier: 4.477A pdb=" N ASP S 171 " --> pdb=" O LYS S 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 131 removed outlier: 3.517A pdb=" N LYS S 128 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 179 through 183 removed outlier: 6.618A pdb=" N LEU S 180 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 195 through 199 removed outlier: 5.654A pdb=" N ILE S 195 " --> pdb=" O LYS S 211 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS S 211 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS S 197 " --> pdb=" O HIS S 209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 12 through 17 removed outlier: 6.485A pdb=" N LYS T 2 " --> pdb=" O LEU T 109 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU T 111 " --> pdb=" O LYS T 2 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ASN T 4 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE T 113 " --> pdb=" O ASN T 4 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER T 6 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS T 115 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY T 54 " --> pdb=" O ALA T 110 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL T 112 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE T 52 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL T 114 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE T 50 " --> pdb=" O VAL T 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 72 through 77 Processing sheet with id=AB8, first strand: chain 'T' and resid 162 through 163 Processing sheet with id=AB9, first strand: chain 'U' and resid 45 through 49 removed outlier: 6.623A pdb=" N LYS U 56 " --> pdb=" O HIS U 89 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE U 91 " --> pdb=" O LYS U 56 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU U 58 " --> pdb=" O ILE U 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU U 93 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE U 60 " --> pdb=" O LEU U 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 180 through 184 removed outlier: 7.097A pdb=" N LYS U 148 " --> pdb=" O GLN U 180 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N VAL U 182 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN U 150 " --> pdb=" O VAL U 182 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU U 184 " --> pdb=" O GLN U 150 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL U 152 " --> pdb=" O GLU U 184 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY U 137 " --> pdb=" O LEU U 153 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS U 138 " --> pdb=" O ASP b 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP b 54 " --> pdb=" O LYS U 138 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE b 50 " --> pdb=" O TYR U 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 3 through 4 removed outlier: 3.915A pdb=" N ILE V 3 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 42 through 48 removed outlier: 4.106A pdb=" N THR V 48 " --> pdb=" O ASN V 52 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASN V 52 " --> pdb=" O THR V 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 62 through 67 removed outlier: 6.535A pdb=" N GLN V 103 " --> pdb=" O ALA V 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL V 81 " --> pdb=" O ILE V 101 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY V 181 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN V 64 " --> pdb=" O GLY V 181 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE V 183 " --> pdb=" O ASN V 64 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER V 66 " --> pdb=" O ILE V 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 70 through 77 removed outlier: 18.062A pdb=" N ILE X 70 " --> pdb=" O LEU X 91 " (cutoff:3.500A) removed outlier: 15.217A pdb=" N LEU X 91 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N THR X 72 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA X 89 " --> pdb=" O THR X 72 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL X 85 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE X 137 " --> pdb=" O ASN X 106 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL X 139 " --> pdb=" O PRO X 108 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS X 110 " --> pdb=" O VAL X 139 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N LYS X 141 " --> pdb=" O HIS X 110 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL X 139 " --> pdb=" O GLY X 126 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY X 126 " --> pdb=" O VAL X 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 32 through 39 removed outlier: 3.669A pdb=" N LYS a 38 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU a 49 " --> pdb=" O LYS a 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 72 through 74 Processing sheet with id=AC8, first strand: chain 'b' and resid 72 through 74 removed outlier: 5.361A pdb=" N ILE b 125 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR b 105 " --> pdb=" O ILE b 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 130 through 131 removed outlier: 6.477A pdb=" N LEU c 103 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL c 127 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU c 101 " --> pdb=" O VAL c 127 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG c 73 " --> pdb=" O LEU c 54 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS c 56 " --> pdb=" O CYS c 71 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS c 71 " --> pdb=" O LYS c 56 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE c 122 " --> pdb=" O THR c 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 8 through 15 removed outlier: 4.339A pdb=" N VAL d 12 " --> pdb=" O GLN d 22 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN d 22 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER d 14 " --> pdb=" O ARG d 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG d 20 " --> pdb=" O SER d 14 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL d 70 " --> pdb=" O PHE d 60 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 44 through 47 Processing sheet with id=AD3, first strand: chain 'f' and resid 64 through 65 removed outlier: 3.628A pdb=" N LYS f 72 " --> pdb=" O THR f 65 " (cutoff:3.500A) 867 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 856 hydrogen bonds 1366 hydrogen bond angles 0 basepair planarities 354 basepair parallelities 621 stacking parallelities Total time for adding SS restraints: 13.71 Time building geometry restraints manager: 4.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5160 1.31 - 1.44: 19727 1.44 - 1.56: 21809 1.56 - 1.69: 2373 1.69 - 1.81: 48 Bond restraints: 49117 Sorted by residual: bond pdb=" CA LYS a 5 " pdb=" CB LYS a 5 " ideal model delta sigma weight residual 1.524 1.602 -0.078 1.62e-02 3.81e+03 2.33e+01 bond pdb=" CB PRO R 85 " pdb=" CG PRO R 85 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.63e+00 bond pdb=" CB ASN Y 138 " pdb=" CG ASN Y 138 " ideal model delta sigma weight residual 1.516 1.583 -0.067 2.50e-02 1.60e+03 7.09e+00 bond pdb=" N ASN S 96 " pdb=" CA ASN S 96 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.34e+00 bond pdb=" N PRO R 85 " pdb=" CA PRO R 85 " ideal model delta sigma weight residual 1.468 1.438 0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 49112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 71588 4.66 - 9.32: 478 9.32 - 13.98: 33 13.98 - 18.64: 3 18.64 - 23.30: 2 Bond angle restraints: 72104 Sorted by residual: angle pdb=" CA PRO R 85 " pdb=" N PRO R 85 " pdb=" CD PRO R 85 " ideal model delta sigma weight residual 112.00 96.19 15.81 1.40e+00 5.10e-01 1.28e+02 angle pdb=" N VAL P 139 " pdb=" CA VAL P 139 " pdb=" C VAL P 139 " ideal model delta sigma weight residual 112.43 106.10 6.33 9.20e-01 1.18e+00 4.74e+01 angle pdb=" CA LEU V 193 " pdb=" CB LEU V 193 " pdb=" CG LEU V 193 " ideal model delta sigma weight residual 116.30 139.60 -23.30 3.50e+00 8.16e-02 4.43e+01 angle pdb=" CA GLU d 51 " pdb=" CB GLU d 51 " pdb=" CG GLU d 51 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.04e+01 angle pdb=" N GLY S 193 " pdb=" CA GLY S 193 " pdb=" C GLY S 193 " ideal model delta sigma weight residual 113.18 127.17 -13.99 2.37e+00 1.78e-01 3.49e+01 ... (remaining 72099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 27736 35.81 - 71.62: 2926 71.62 - 107.43: 316 107.43 - 143.25: 19 143.25 - 179.06: 26 Dihedral angle restraints: 31023 sinusoidal: 23170 harmonic: 7853 Sorted by residual: dihedral pdb=" O4' U 21145 " pdb=" C1' U 21145 " pdb=" N1 U 21145 " pdb=" C2 U 21145 " ideal model delta sinusoidal sigma weight residual -160.00 16.60 -176.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21082 " pdb=" C1' C 21082 " pdb=" N1 C 21082 " pdb=" C2 C 21082 " ideal model delta sinusoidal sigma weight residual -160.00 11.30 -171.30 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 2 767 " pdb=" C1' U 2 767 " pdb=" N1 U 2 767 " pdb=" C2 U 2 767 " ideal model delta sinusoidal sigma weight residual 200.00 38.79 161.21 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 31020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 8947 0.137 - 0.273: 148 0.273 - 0.410: 16 0.410 - 0.547: 1 0.547 - 0.684: 1 Chirality restraints: 9113 Sorted by residual: chirality pdb=" CG LEU P 176 " pdb=" CB LEU P 176 " pdb=" CD1 LEU P 176 " pdb=" CD2 LEU P 176 " both_signs ideal model delta sigma weight residual False -2.59 -1.91 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CB ILE R 218 " pdb=" CA ILE R 218 " pdb=" CG1 ILE R 218 " pdb=" CG2 ILE R 218 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB ILE Y 37 " pdb=" CA ILE Y 37 " pdb=" CG1 ILE Y 37 " pdb=" CG2 ILE Y 37 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 9110 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 84 " -0.138 5.00e-02 4.00e+02 1.92e-01 5.87e+01 pdb=" N PRO R 85 " 0.330 5.00e-02 4.00e+02 pdb=" CA PRO R 85 " -0.106 5.00e-02 4.00e+02 pdb=" CD PRO R 85 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP W 151 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" CG ASP W 151 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP W 151 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP W 151 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU a 10 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C GLU a 10 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU a 10 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU a 11 " 0.016 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 6758 2.75 - 3.29: 39385 3.29 - 3.83: 92808 3.83 - 4.36: 107778 4.36 - 4.90: 152051 Nonbonded interactions: 398780 Sorted by model distance: nonbonded pdb=" O6 G 21658 " pdb=" O2 U 21743 " model vdw 2.217 2.432 nonbonded pdb=" OP1 G 2 388 " pdb=" O2' G 2 423 " model vdw 2.224 3.040 nonbonded pdb=" O6 G 21697 " pdb=" O4 U 21704 " model vdw 2.270 2.432 nonbonded pdb=" OG1 THR P 10 " pdb=" OD2 ASP P 13 " model vdw 2.272 3.040 nonbonded pdb=" O GLN U 74 " pdb=" OG1 THR U 78 " model vdw 2.272 3.040 ... (remaining 398775 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=0.55 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 46.420 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.005 0.138 49117 Z= 0.247 Angle : 0.977 23.297 72104 Z= 0.499 Chirality : 0.048 0.684 9113 Planarity : 0.008 0.192 4839 Dihedral : 23.133 179.057 25945 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.68 % Allowed : 23.89 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.10 (0.14), residues: 2685 helix: -1.65 (0.14), residues: 909 sheet: -0.33 (0.24), residues: 434 loop : -1.50 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG X 116 TYR 0.031 0.003 TYR S 103 PHE 0.029 0.002 PHE R 57 TRP 0.014 0.002 TRP P 174 HIS 0.014 0.002 HIS b 44 Details of bonding type rmsd covalent geometry : bond 0.00494 (49117) covalent geometry : angle 0.97745 (72104) hydrogen bonds : bond 0.11841 ( 1721) hydrogen bonds : angle 5.65183 ( 3823) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 421 time to evaluate : 1.020 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: x 16 ILE cc_start: 0.7611 (mp) cc_final: 0.7368 (pp) REVERT: x 41 SER cc_start: 0.7624 (p) cc_final: 0.6764 (p) REVERT: x 55 ASP cc_start: 0.8359 (m-30) cc_final: 0.8151 (m-30) REVERT: x 126 LEU cc_start: 0.8937 (mm) cc_final: 0.8683 (mm) REVERT: P 49 ASN cc_start: 0.8898 (t0) cc_final: 0.8356 (t0) REVERT: P 125 ASP cc_start: 0.8171 (t0) cc_final: 0.7781 (t0) REVERT: R 98 PHE cc_start: 0.8520 (m-80) cc_final: 0.8192 (m-10) REVERT: S 121 TYR cc_start: 0.8563 (p90) cc_final: 0.8228 (p90) REVERT: S 230 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7806 (pp20) REVERT: S 251 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7931 (tm-30) REVERT: T 127 THR cc_start: 0.9091 (p) cc_final: 0.8874 (t) REVERT: U 43 PHE cc_start: 0.8372 (p90) cc_final: 0.8054 (p90) REVERT: V 117 TYR cc_start: 0.9025 (m-80) cc_final: 0.8821 (m-80) REVERT: V 192 TYR cc_start: 0.8664 (m-80) cc_final: 0.8439 (m-80) REVERT: X 30 ARG cc_start: 0.7056 (mmm160) cc_final: 0.6667 (mmm160) REVERT: b 83 ILE cc_start: 0.7641 (mm) cc_final: 0.7219 (mm) REVERT: f 82 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8358 (ptmm) outliers start: 14 outliers final: 1 residues processed: 428 average time/residue: 0.7034 time to fit residues: 379.0468 Evaluate side-chains 352 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 163 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 37 GLN x 300 HIS ** R 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 GLN R 189 GLN ** S 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 130 GLN S 197 HIS ** S 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 ASN W 124 HIS X 14 GLN X 118 GLN Y 21 ASN Y 78 ASN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN ** a 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN d 31 ASN g 17 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065333 restraints weight = 162116.530| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.93 r_work: 0.3112 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 49117 Z= 0.130 Angle : 0.621 14.484 72104 Z= 0.320 Chirality : 0.037 0.326 9113 Planarity : 0.005 0.096 4839 Dihedral : 23.609 179.670 21057 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.19 % Allowed : 23.16 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 2685 helix: -0.17 (0.16), residues: 933 sheet: -0.32 (0.24), residues: 459 loop : -1.35 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 90 TYR 0.018 0.001 TYR a 50 PHE 0.036 0.001 PHE P 38 TRP 0.007 0.001 TRP c 24 HIS 0.005 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00262 (49117) covalent geometry : angle 0.62132 (72104) hydrogen bonds : bond 0.05387 ( 1721) hydrogen bonds : angle 4.28114 ( 3823) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 384 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7500 (mpt) REVERT: x 53 LEU cc_start: 0.9289 (mt) cc_final: 0.8988 (pp) REVERT: x 54 GLN cc_start: 0.8284 (tp40) cc_final: 0.8028 (tp40) REVERT: x 62 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8832 (mm-30) REVERT: x 92 GLN cc_start: 0.7209 (pm20) cc_final: 0.6714 (pm20) REVERT: P 125 ASP cc_start: 0.8440 (t0) cc_final: 0.8204 (t0) REVERT: R 98 PHE cc_start: 0.8466 (m-80) cc_final: 0.8212 (m-80) REVERT: S 118 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: S 121 TYR cc_start: 0.8856 (p90) cc_final: 0.8576 (p90) REVERT: S 230 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8005 (pp20) REVERT: S 251 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8440 (tm-30) REVERT: U 43 PHE cc_start: 0.8508 (p90) cc_final: 0.8021 (p90) REVERT: U 80 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: V 117 TYR cc_start: 0.9162 (m-80) cc_final: 0.8850 (m-80) REVERT: X 55 ASP cc_start: 0.8333 (t0) cc_final: 0.8126 (t70) REVERT: X 116 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (tmm-80) REVERT: Y 49 GLN cc_start: 0.8995 (mt0) cc_final: 0.8734 (mt0) REVERT: Y 107 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7931 (mmmm) REVERT: a 52 THR cc_start: 0.8915 (m) cc_final: 0.8709 (m) REVERT: a 58 TYR cc_start: 0.8226 (t80) cc_final: 0.7916 (t80) REVERT: d 42 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8651 (tm-30) REVERT: f 82 LYS cc_start: 0.8585 (ttpt) cc_final: 0.8123 (ptmt) outliers start: 66 outliers final: 19 residues processed: 416 average time/residue: 0.6717 time to fit residues: 355.0003 Evaluate side-chains 361 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 34 MET Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain T residue 127 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 116 ARG Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 107 LYS Chi-restraints excluded: chain b residue 83 ILE Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 125 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 192 optimal weight: 0.2980 chunk 170 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 355 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS P 23 HIS R 147 ASN R 152 HIS R 189 GLN S 130 GLN S 201 HIS T 182 GLN U 71 HIS W 123 HIS ** X 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 12 ASN b 15 ASN b 64 GLN c 22 ASN f 19 HIS g 57 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.090573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060073 restraints weight = 162527.849| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.00 r_work: 0.2966 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 49117 Z= 0.351 Angle : 0.755 14.378 72104 Z= 0.388 Chirality : 0.043 0.370 9113 Planarity : 0.006 0.105 4839 Dihedral : 23.678 178.769 21055 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.88 % Allowed : 23.45 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2685 helix: 0.40 (0.17), residues: 937 sheet: -0.50 (0.24), residues: 463 loop : -1.33 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG x 43 TYR 0.026 0.002 TYR X 97 PHE 0.029 0.002 PHE P 38 TRP 0.014 0.002 TRP c 24 HIS 0.007 0.002 HIS S 201 Details of bonding type rmsd covalent geometry : bond 0.00707 (49117) covalent geometry : angle 0.75496 (72104) hydrogen bonds : bond 0.07257 ( 1721) hydrogen bonds : angle 4.29791 ( 3823) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 354 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 42 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7551 (mttm) REVERT: x 45 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: x 53 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9078 (pp) REVERT: x 54 GLN cc_start: 0.8627 (tp40) cc_final: 0.8405 (tp40) REVERT: x 89 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7756 (tt) REVERT: x 92 GLN cc_start: 0.6933 (pm20) cc_final: 0.6206 (pm20) REVERT: P 77 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8720 (t) REVERT: P 117 GLU cc_start: 0.8864 (pp20) cc_final: 0.8650 (pp20) REVERT: R 40 LYS cc_start: 0.9237 (mttp) cc_final: 0.8882 (mppt) REVERT: S 82 TYR cc_start: 0.9239 (t80) cc_final: 0.9027 (t80) REVERT: S 118 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: S 153 ASN cc_start: 0.8574 (m-40) cc_final: 0.8265 (m-40) REVERT: S 197 HIS cc_start: 0.9122 (OUTLIER) cc_final: 0.8831 (p-80) REVERT: S 230 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7954 (pp20) REVERT: S 251 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8308 (tm-30) REVERT: T 127 THR cc_start: 0.9256 (p) cc_final: 0.9038 (t) REVERT: U 43 PHE cc_start: 0.8666 (p90) cc_final: 0.8229 (p90) REVERT: V 107 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8531 (p) REVERT: V 117 TYR cc_start: 0.9265 (m-80) cc_final: 0.8958 (m-80) REVERT: V 192 TYR cc_start: 0.8982 (m-80) cc_final: 0.8767 (m-80) REVERT: X 55 ASP cc_start: 0.8652 (t0) cc_final: 0.8366 (t0) REVERT: a 52 THR cc_start: 0.9109 (m) cc_final: 0.8860 (m) REVERT: b 49 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: b 83 ILE cc_start: 0.8082 (mm) cc_final: 0.7824 (mm) REVERT: b 104 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8992 (pp) REVERT: d 42 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8692 (tm-30) REVERT: f 82 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8072 (ptmt) outliers start: 101 outliers final: 45 residues processed: 418 average time/residue: 0.6405 time to fit residues: 342.3356 Evaluate side-chains 370 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 45 GLU Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 53 LEU Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 129 ASP Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain S residue 67 GLN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain X residue 44 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 50 TYR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 45 THR Chi-restraints excluded: chain f residue 64 CYS Chi-restraints excluded: chain g residue 49 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 288 optimal weight: 0.9990 chunk 377 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS P 39 ASN S 130 GLN X 118 GLN X 127 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.091641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061554 restraints weight = 163064.641| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.89 r_work: 0.3006 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 49117 Z= 0.235 Angle : 0.663 13.878 72104 Z= 0.341 Chirality : 0.039 0.341 9113 Planarity : 0.005 0.080 4839 Dihedral : 23.611 179.841 21055 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.98 % Allowed : 24.56 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2685 helix: 0.76 (0.17), residues: 938 sheet: -0.50 (0.24), residues: 455 loop : -1.25 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 3 TYR 0.022 0.002 TYR P 110 PHE 0.035 0.002 PHE P 38 TRP 0.010 0.001 TRP c 24 HIS 0.007 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00475 (49117) covalent geometry : angle 0.66313 (72104) hydrogen bonds : bond 0.05853 ( 1721) hydrogen bonds : angle 4.06680 ( 3823) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 348 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8762 (pptt) cc_final: 0.8484 (pptt) REVERT: x 34 MET cc_start: 0.6525 (mpt) cc_final: 0.6263 (mpt) REVERT: x 42 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (mttm) REVERT: x 45 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: x 89 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (tp) REVERT: x 92 GLN cc_start: 0.7030 (pm20) cc_final: 0.6653 (pm20) REVERT: P 117 GLU cc_start: 0.8849 (pp20) cc_final: 0.8531 (pp20) REVERT: R 40 LYS cc_start: 0.9196 (mttp) cc_final: 0.8593 (mtmm) REVERT: R 97 ARG cc_start: 0.8500 (mtm110) cc_final: 0.8080 (mtm180) REVERT: S 118 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: S 153 ASN cc_start: 0.8540 (m-40) cc_final: 0.8267 (m-40) REVERT: S 187 ARG cc_start: 0.8449 (mpp-170) cc_final: 0.8094 (mpp-170) REVERT: S 197 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8417 (p-80) REVERT: S 230 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7991 (pp20) REVERT: S 251 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8419 (tm-30) REVERT: T 127 THR cc_start: 0.9228 (p) cc_final: 0.9021 (t) REVERT: U 43 PHE cc_start: 0.8676 (p90) cc_final: 0.8283 (p90) REVERT: U 80 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8834 (mm-30) REVERT: V 107 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8479 (p) REVERT: V 117 TYR cc_start: 0.9250 (m-80) cc_final: 0.8953 (m-80) REVERT: X 55 ASP cc_start: 0.8536 (t0) cc_final: 0.8247 (t0) REVERT: a 52 THR cc_start: 0.9083 (m) cc_final: 0.8829 (m) REVERT: b 83 ILE cc_start: 0.7893 (mm) cc_final: 0.7626 (mm) REVERT: b 104 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8943 (pp) REVERT: d 38 ASP cc_start: 0.8301 (m-30) cc_final: 0.8067 (t0) REVERT: d 42 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8633 (tm-30) REVERT: d 53 ASP cc_start: 0.8740 (m-30) cc_final: 0.8087 (t0) REVERT: d 96 LEU cc_start: 0.9373 (mm) cc_final: 0.9070 (mm) REVERT: f 82 LYS cc_start: 0.8818 (ttpt) cc_final: 0.7927 (ptmt) REVERT: g 56 MET cc_start: 0.8705 (ppp) cc_final: 0.8405 (ppp) outliers start: 103 outliers final: 49 residues processed: 410 average time/residue: 0.6340 time to fit residues: 333.6376 Evaluate side-chains 380 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 323 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 45 GLU Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 89 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 102 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 64 CYS Chi-restraints excluded: chain f residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 106 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 363 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 37 GLN x 300 HIS S 130 GLN V 52 ASN X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.091865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061148 restraints weight = 162212.776| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.02 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 49117 Z= 0.208 Angle : 0.653 14.579 72104 Z= 0.334 Chirality : 0.039 0.334 9113 Planarity : 0.005 0.071 4839 Dihedral : 23.533 179.568 21055 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.32 % Allowed : 24.81 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2685 helix: 0.87 (0.17), residues: 940 sheet: -0.54 (0.24), residues: 457 loop : -1.20 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 3 TYR 0.021 0.002 TYR P 110 PHE 0.015 0.001 PHE P 38 TRP 0.011 0.001 TRP c 24 HIS 0.005 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00419 (49117) covalent geometry : angle 0.65293 (72104) hydrogen bonds : bond 0.05650 ( 1721) hydrogen bonds : angle 3.97008 ( 3823) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 346 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.6308 (mpt) cc_final: 0.5599 (mpt) REVERT: x 42 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7807 (mttm) REVERT: x 45 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: x 55 ASP cc_start: 0.8608 (m-30) cc_final: 0.8302 (m-30) REVERT: x 56 LYS cc_start: 0.8998 (ptpp) cc_final: 0.8797 (mmpt) REVERT: x 58 LYS cc_start: 0.9115 (tppt) cc_final: 0.8883 (tppt) REVERT: x 92 GLN cc_start: 0.7119 (pm20) cc_final: 0.6889 (pm20) REVERT: S 118 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: S 153 ASN cc_start: 0.8477 (m-40) cc_final: 0.8216 (m-40) REVERT: S 180 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8220 (tt) REVERT: S 187 ARG cc_start: 0.8229 (mpp-170) cc_final: 0.8001 (mpp-170) REVERT: S 197 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.7924 (p-80) REVERT: S 230 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7979 (pp20) REVERT: S 251 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8331 (tm-30) REVERT: U 43 PHE cc_start: 0.8608 (p90) cc_final: 0.8285 (p90) REVERT: U 80 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: V 107 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8379 (p) REVERT: W 41 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: X 55 ASP cc_start: 0.8581 (t0) cc_final: 0.8328 (t0) REVERT: Y 103 GLU cc_start: 0.8215 (pp20) cc_final: 0.8000 (pp20) REVERT: a 52 THR cc_start: 0.9064 (m) cc_final: 0.8840 (m) REVERT: b 49 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: b 104 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8717 (pp) REVERT: d 18 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9260 (mm) REVERT: d 42 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8302 (tm-30) REVERT: d 46 GLU cc_start: 0.8371 (pm20) cc_final: 0.8069 (pm20) REVERT: d 53 ASP cc_start: 0.8513 (m-30) cc_final: 0.8012 (t0) REVERT: d 96 LEU cc_start: 0.9368 (mm) cc_final: 0.9040 (mm) REVERT: f 82 LYS cc_start: 0.8810 (ttpt) cc_final: 0.7918 (ptmt) outliers start: 110 outliers final: 57 residues processed: 418 average time/residue: 0.6272 time to fit residues: 335.8004 Evaluate side-chains 392 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 324 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 45 GLU Chi-restraints excluded: chain x residue 53 LEU Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 41 GLU Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 49 GLU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain f residue 64 CYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 17 optimal weight: 40.0000 chunk 116 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 380 optimal weight: 0.0570 chunk 174 optimal weight: 8.9990 chunk 375 optimal weight: 6.9990 chunk 360 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 300 HIS S 130 GLN ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN d 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.092113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062216 restraints weight = 161287.016| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.87 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 49117 Z= 0.186 Angle : 0.635 13.828 72104 Z= 0.326 Chirality : 0.038 0.327 9113 Planarity : 0.005 0.067 4839 Dihedral : 23.483 179.789 21055 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.03 % Allowed : 25.92 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2685 helix: 0.97 (0.17), residues: 939 sheet: -0.56 (0.23), residues: 458 loop : -1.17 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 87 TYR 0.020 0.002 TYR P 110 PHE 0.032 0.001 PHE R 66 TRP 0.009 0.001 TRP c 24 HIS 0.005 0.001 HIS T 22 Details of bonding type rmsd covalent geometry : bond 0.00375 (49117) covalent geometry : angle 0.63536 (72104) hydrogen bonds : bond 0.05448 ( 1721) hydrogen bonds : angle 3.93470 ( 3823) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 343 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.6367 (mpt) cc_final: 0.5606 (mpt) REVERT: x 42 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7764 (mmtm) REVERT: x 45 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: x 56 LYS cc_start: 0.9031 (ptpp) cc_final: 0.8824 (mmpt) REVERT: x 92 GLN cc_start: 0.7162 (pm20) cc_final: 0.6812 (pm20) REVERT: P 125 ASP cc_start: 0.8321 (t0) cc_final: 0.8102 (t0) REVERT: P 157 ASP cc_start: 0.8300 (t0) cc_final: 0.8032 (t0) REVERT: R 55 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: R 97 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7729 (mtp85) REVERT: R 194 GLU cc_start: 0.8558 (mp0) cc_final: 0.8321 (mp0) REVERT: S 118 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: S 153 ASN cc_start: 0.8536 (m-40) cc_final: 0.8258 (m-40) REVERT: S 197 HIS cc_start: 0.9058 (OUTLIER) cc_final: 0.8126 (p-80) REVERT: S 230 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7995 (pp20) REVERT: S 251 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8441 (tm-30) REVERT: U 80 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8854 (mm-30) REVERT: V 192 TYR cc_start: 0.8850 (m-80) cc_final: 0.8580 (m-80) REVERT: X 55 ASP cc_start: 0.8613 (t0) cc_final: 0.8353 (t0) REVERT: Y 4 MET cc_start: 0.7822 (pmm) cc_final: 0.7509 (ptp) REVERT: Y 103 GLU cc_start: 0.8297 (pp20) cc_final: 0.8060 (pp20) REVERT: a 21 ASN cc_start: 0.8828 (t0) cc_final: 0.8534 (t0) REVERT: a 34 ILE cc_start: 0.9268 (mp) cc_final: 0.9028 (mt) REVERT: a 52 THR cc_start: 0.9057 (m) cc_final: 0.8849 (m) REVERT: b 104 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8919 (pp) REVERT: d 18 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9259 (mm) REVERT: d 42 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8572 (tm-30) REVERT: d 46 GLU cc_start: 0.8467 (pm20) cc_final: 0.8205 (pm20) REVERT: f 82 LYS cc_start: 0.8928 (ttpt) cc_final: 0.7994 (ptmt) REVERT: g 55 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7726 (mmm-85) outliers start: 104 outliers final: 66 residues processed: 411 average time/residue: 0.6103 time to fit residues: 323.6727 Evaluate side-chains 398 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 42 LYS Chi-restraints excluded: chain x residue 45 GLU Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 153 SER Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain Y residue 134 VAL Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 64 CYS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 225 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 145 optimal weight: 50.0000 chunk 264 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 277 optimal weight: 0.9980 chunk 352 optimal weight: 5.9990 chunk 304 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 300 HIS P 33 GLN P 39 ASN R 189 GLN S 130 GLN V 52 ASN V 111 GLN ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 64 GLN d 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.092265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062295 restraints weight = 161000.087| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.88 r_work: 0.3029 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 49117 Z= 0.175 Angle : 0.641 14.560 72104 Z= 0.327 Chirality : 0.038 0.321 9113 Planarity : 0.005 0.065 4839 Dihedral : 23.435 179.926 21055 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.17 % Allowed : 26.31 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2685 helix: 1.03 (0.17), residues: 934 sheet: -0.53 (0.24), residues: 459 loop : -1.12 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Y 104 TYR 0.022 0.002 TYR P 110 PHE 0.045 0.001 PHE P 38 TRP 0.009 0.001 TRP c 24 HIS 0.005 0.001 HIS P 32 Details of bonding type rmsd covalent geometry : bond 0.00354 (49117) covalent geometry : angle 0.64072 (72104) hydrogen bonds : bond 0.05358 ( 1721) hydrogen bonds : angle 3.92588 ( 3823) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 345 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 25 LYS cc_start: 0.8717 (pptt) cc_final: 0.8467 (pptt) REVERT: x 34 MET cc_start: 0.6615 (mpt) cc_final: 0.5873 (mpt) REVERT: x 55 ASP cc_start: 0.8537 (m-30) cc_final: 0.8229 (m-30) REVERT: x 92 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: P 125 ASP cc_start: 0.8373 (t0) cc_final: 0.8096 (t0) REVERT: R 55 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: R 97 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7871 (mtm110) REVERT: R 194 GLU cc_start: 0.8527 (mp0) cc_final: 0.8306 (mp0) REVERT: S 118 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: S 153 ASN cc_start: 0.8554 (m-40) cc_final: 0.8266 (m-40) REVERT: S 180 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8263 (tt) REVERT: S 187 ARG cc_start: 0.8415 (mpp-170) cc_final: 0.8050 (mtm180) REVERT: S 197 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8161 (p-80) REVERT: S 230 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7986 (pp20) REVERT: S 251 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8481 (tm-30) REVERT: T 1 MET cc_start: 0.9053 (tpp) cc_final: 0.8365 (ttm) REVERT: U 80 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8824 (mm-30) REVERT: V 192 TYR cc_start: 0.8921 (m-80) cc_final: 0.8643 (m-80) REVERT: X 55 ASP cc_start: 0.8609 (t0) cc_final: 0.8342 (t0) REVERT: Y 4 MET cc_start: 0.7848 (pmm) cc_final: 0.7630 (ptp) REVERT: b 104 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8929 (pp) REVERT: d 18 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9251 (mm) REVERT: d 42 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8496 (tm-30) REVERT: d 46 GLU cc_start: 0.8462 (pm20) cc_final: 0.8240 (pm20) REVERT: d 53 ASP cc_start: 0.8736 (m-30) cc_final: 0.8528 (t0) REVERT: d 63 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8212 (tp40) REVERT: f 42 ASN cc_start: 0.9067 (m110) cc_final: 0.8769 (m110) REVERT: f 82 LYS cc_start: 0.8976 (ttpt) cc_final: 0.7974 (ptmt) REVERT: g 55 ARG cc_start: 0.8106 (tpt-90) cc_final: 0.7849 (mmm-85) outliers start: 107 outliers final: 71 residues processed: 418 average time/residue: 0.4437 time to fit residues: 241.2787 Evaluate side-chains 410 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 331 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 48 SER Chi-restraints excluded: chain x residue 53 LEU Chi-restraints excluded: chain x residue 92 GLN Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 149 LEU Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 196 VAL Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain T residue 227 ARG Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 147 ASN Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 107 PHE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 89 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 304 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS S 57 ASN S 130 GLN ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 21 ASN b 15 ASN b 64 GLN d 113 ASN g 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061213 restraints weight = 162344.177| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.92 r_work: 0.2995 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 49117 Z= 0.241 Angle : 0.685 14.371 72104 Z= 0.349 Chirality : 0.040 0.330 9113 Planarity : 0.005 0.087 4839 Dihedral : 23.429 179.638 21055 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.55 % Allowed : 27.47 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2685 helix: 0.99 (0.17), residues: 934 sheet: -0.59 (0.24), residues: 459 loop : -1.15 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 104 TYR 0.020 0.002 TYR P 110 PHE 0.030 0.002 PHE Y 26 TRP 0.010 0.001 TRP c 24 HIS 0.005 0.001 HIS b 44 Details of bonding type rmsd covalent geometry : bond 0.00486 (49117) covalent geometry : angle 0.68522 (72104) hydrogen bonds : bond 0.05830 ( 1721) hydrogen bonds : angle 4.03934 ( 3823) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 332 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.6699 (mpt) cc_final: 0.6067 (mpt) REVERT: x 92 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6848 (pm20) REVERT: P 77 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8849 (t) REVERT: P 125 ASP cc_start: 0.8378 (t0) cc_final: 0.8111 (t0) REVERT: R 55 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: R 66 PHE cc_start: 0.8957 (p90) cc_final: 0.8683 (p90) REVERT: R 70 ASP cc_start: 0.9032 (p0) cc_final: 0.8788 (p0) REVERT: R 97 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7823 (mtm180) REVERT: R 194 GLU cc_start: 0.8585 (mp0) cc_final: 0.8354 (mp0) REVERT: S 118 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: S 153 ASN cc_start: 0.8600 (m-40) cc_final: 0.8316 (m-40) REVERT: S 180 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8327 (tt) REVERT: S 197 HIS cc_start: 0.9060 (OUTLIER) cc_final: 0.8160 (p-80) REVERT: S 230 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8014 (pp20) REVERT: S 251 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8511 (tm-30) REVERT: T 1 MET cc_start: 0.9032 (tpp) cc_final: 0.8405 (ttm) REVERT: U 80 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8832 (mm-30) REVERT: X 55 ASP cc_start: 0.8525 (t0) cc_final: 0.8259 (t0) REVERT: b 104 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8973 (pp) REVERT: d 18 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9267 (mm) REVERT: d 38 ASP cc_start: 0.8319 (t0) cc_final: 0.8087 (t0) REVERT: d 42 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8365 (tm-30) REVERT: d 46 GLU cc_start: 0.8468 (pm20) cc_final: 0.8222 (pm20) REVERT: d 53 ASP cc_start: 0.8729 (m-30) cc_final: 0.8451 (t0) REVERT: f 82 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8008 (ptmt) REVERT: g 55 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.7892 (mmm-85) outliers start: 94 outliers final: 67 residues processed: 396 average time/residue: 0.3820 time to fit residues: 197.5498 Evaluate side-chains 396 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 320 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 53 LEU Chi-restraints excluded: chain x residue 92 GLN Chi-restraints excluded: chain x residue 126 LEU Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 147 THR Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 196 VAL Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain S residue 227 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 14 THR Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 94 ASP Chi-restraints excluded: chain W residue 148 VAL Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 67 THR Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain c residue 59 ILE Chi-restraints excluded: chain c residue 117 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 64 CYS Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 266 optimal weight: 0.8980 chunk 284 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 21 optimal weight: 50.0000 chunk 169 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 232 optimal weight: 0.4980 chunk 135 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 37 GLN x 47 ASN ** x 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS P 39 ASN S 130 GLN V 52 ASN W 38 ASN ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN a 7 GLN a 21 ASN b 15 ASN b 64 GLN d 113 ASN ** f 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.093765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063921 restraints weight = 160478.123| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.98 r_work: 0.3081 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 49117 Z= 0.122 Angle : 0.642 17.808 72104 Z= 0.324 Chirality : 0.036 0.320 9113 Planarity : 0.004 0.062 4839 Dihedral : 23.362 179.738 21055 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.05 % Allowed : 29.30 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2685 helix: 1.08 (0.17), residues: 929 sheet: -0.52 (0.24), residues: 460 loop : -1.06 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 227 TYR 0.024 0.001 TYR a 50 PHE 0.051 0.001 PHE P 38 TRP 0.012 0.001 TRP V 112 HIS 0.031 0.001 HIS x 20 Details of bonding type rmsd covalent geometry : bond 0.00251 (49117) covalent geometry : angle 0.64235 (72104) hydrogen bonds : bond 0.05042 ( 1721) hydrogen bonds : angle 3.90656 ( 3823) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 359 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.6492 (mpt) cc_final: 0.5780 (mpt) REVERT: x 53 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9102 (pp) REVERT: x 92 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7101 (pm20) REVERT: P 125 ASP cc_start: 0.8350 (t0) cc_final: 0.8044 (t0) REVERT: R 55 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: R 70 ASP cc_start: 0.8877 (p0) cc_final: 0.8643 (p0) REVERT: R 97 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7774 (mtp85) REVERT: R 119 LYS cc_start: 0.9022 (pptt) cc_final: 0.8742 (ptpt) REVERT: R 194 GLU cc_start: 0.8535 (mp0) cc_final: 0.8328 (mp0) REVERT: S 153 ASN cc_start: 0.8515 (m-40) cc_final: 0.8238 (m-40) REVERT: S 197 HIS cc_start: 0.9027 (OUTLIER) cc_final: 0.8151 (p-80) REVERT: S 230 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7963 (pp20) REVERT: S 251 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8497 (tm-30) REVERT: T 1 MET cc_start: 0.9049 (tpp) cc_final: 0.8476 (ttm) REVERT: U 80 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8834 (mm-30) REVERT: W 77 ILE cc_start: 0.9296 (pp) cc_final: 0.8939 (pp) REVERT: X 55 ASP cc_start: 0.8535 (t0) cc_final: 0.8279 (t0) REVERT: X 116 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7392 (tmm-80) REVERT: a 21 ASN cc_start: 0.8559 (t0) cc_final: 0.8087 (t0) REVERT: d 18 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9231 (mm) REVERT: d 42 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8276 (tm-30) REVERT: d 46 GLU cc_start: 0.8452 (pm20) cc_final: 0.8192 (pm20) REVERT: d 53 ASP cc_start: 0.8725 (m-30) cc_final: 0.8523 (t0) REVERT: f 42 ASN cc_start: 0.9021 (m110) cc_final: 0.8624 (m110) REVERT: f 82 LYS cc_start: 0.8949 (ttpt) cc_final: 0.7906 (ptmt) outliers start: 63 outliers final: 39 residues processed: 402 average time/residue: 0.3804 time to fit residues: 199.9410 Evaluate side-chains 377 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 331 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 53 LEU Chi-restraints excluded: chain x residue 92 GLN Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 39 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 162 CYS Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 196 VAL Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain X residue 116 ARG Chi-restraints excluded: chain X residue 118 GLN Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 117 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 295 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 372 optimal weight: 8.9990 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN ** x 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS R 189 GLN S 130 GLN ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN d 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.090102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059669 restraints weight = 163208.602| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.14 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 49117 Z= 0.344 Angle : 0.764 15.000 72104 Z= 0.389 Chirality : 0.043 0.349 9113 Planarity : 0.006 0.090 4839 Dihedral : 23.416 179.296 21055 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.66 % Allowed : 30.17 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2685 helix: 0.86 (0.17), residues: 927 sheet: -0.61 (0.24), residues: 458 loop : -1.20 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 227 TYR 0.023 0.002 TYR P 110 PHE 0.060 0.002 PHE P 38 TRP 0.013 0.001 TRP c 24 HIS 0.022 0.002 HIS x 20 Details of bonding type rmsd covalent geometry : bond 0.00692 (49117) covalent geometry : angle 0.76365 (72104) hydrogen bonds : bond 0.06855 ( 1721) hydrogen bonds : angle 4.20108 ( 3823) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5370 Ramachandran restraints generated. 2685 Oldfield, 0 Emsley, 2685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 34 MET cc_start: 0.6756 (mpt) cc_final: 0.6010 (mpt) REVERT: x 92 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: P 77 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8725 (t) REVERT: P 125 ASP cc_start: 0.8447 (t0) cc_final: 0.8165 (t0) REVERT: R 55 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: R 70 ASP cc_start: 0.8838 (p0) cc_final: 0.8607 (p0) REVERT: R 95 ARG cc_start: 0.6868 (tmm160) cc_final: 0.6406 (tmm160) REVERT: R 97 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7722 (mtm180) REVERT: R 194 GLU cc_start: 0.8430 (mp0) cc_final: 0.8135 (mp0) REVERT: S 153 ASN cc_start: 0.8510 (m-40) cc_final: 0.8238 (m-40) REVERT: S 197 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.7931 (p-80) REVERT: S 251 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8448 (tm-30) REVERT: T 1 MET cc_start: 0.9038 (tpp) cc_final: 0.8549 (ttm) REVERT: U 80 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8570 (mm-30) REVERT: U 183 PHE cc_start: 0.8415 (m-80) cc_final: 0.8127 (m-80) REVERT: W 77 ILE cc_start: 0.9309 (pp) cc_final: 0.8934 (pp) REVERT: X 55 ASP cc_start: 0.8651 (t0) cc_final: 0.8380 (t0) REVERT: Y 109 LYS cc_start: 0.9322 (mtpt) cc_final: 0.9115 (mtpt) REVERT: a 52 THR cc_start: 0.8905 (m) cc_final: 0.8635 (m) REVERT: d 38 ASP cc_start: 0.8155 (t70) cc_final: 0.7915 (t0) REVERT: d 42 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8552 (tm-30) REVERT: f 82 LYS cc_start: 0.8995 (ttpt) cc_final: 0.7867 (ptmt) REVERT: g 31 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.7903 (mmmt) REVERT: g 56 MET cc_start: 0.8739 (ppp) cc_final: 0.8340 (ppp) outliers start: 55 outliers final: 39 residues processed: 364 average time/residue: 0.3893 time to fit residues: 184.7758 Evaluate side-chains 357 residues out of total 2330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 312 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 92 GLN Chi-restraints excluded: chain x residue 129 ARG Chi-restraints excluded: chain x residue 178 SER Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 106 SER Chi-restraints excluded: chain P residue 162 CYS Chi-restraints excluded: chain P residue 176 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 197 HIS Chi-restraints excluded: chain S residue 208 VAL Chi-restraints excluded: chain S residue 220 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 162 VAL Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 169 TYR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 80 GLU Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain X residue 140 VAL Chi-restraints excluded: chain Y residue 103 GLU Chi-restraints excluded: chain a residue 12 TYR Chi-restraints excluded: chain d residue 28 LEU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 88 THR Chi-restraints excluded: chain f residue 2 VAL Chi-restraints excluded: chain f residue 9 HIS Chi-restraints excluded: chain f residue 77 THR Chi-restraints excluded: chain g residue 31 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 35 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 351 optimal weight: 0.9980 chunk 15 optimal weight: 40.0000 chunk 252 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 377 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 47 ASN ** x 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 300 HIS ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 ASN S 130 GLN ** W 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 GLN ** Y 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN b 64 GLN f 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061154 restraints weight = 161762.923| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.88 r_work: 0.2998 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 49117 Z= 0.209 Angle : 0.697 15.114 72104 Z= 0.355 Chirality : 0.040 0.384 9113 Planarity : 0.005 0.070 4839 Dihedral : 23.417 179.934 21055 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.90 % Allowed : 30.71 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2685 helix: 0.86 (0.17), residues: 931 sheet: -0.54 (0.24), residues: 456 loop : -1.19 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 227 TYR 0.023 0.002 TYR P 110 PHE 0.057 0.002 PHE P 38 TRP 0.009 0.001 TRP c 24 HIS 0.014 0.001 HIS x 20 Details of bonding type rmsd covalent geometry : bond 0.00426 (49117) covalent geometry : angle 0.69659 (72104) hydrogen bonds : bond 0.05790 ( 1721) hydrogen bonds : angle 4.08118 ( 3823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14210.58 seconds wall clock time: 242 minutes 45.78 seconds (14565.78 seconds total)