Starting phenix.real_space_refine on Fri Sep 19 01:43:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwv_32874/09_2025/7wwv_32874.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3121 atoms to isotropic. 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 117 5.49 5 S 67 5.16 5 C 11978 2.51 5 N 3358 2.21 5 O 4102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19622 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1431 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "B" Number of atoms: 1924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Conformer: "B" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} bond proxies already assigned to first conformer: 1950 Chain: "C" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 811 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 22, 'rna3p': 16} Chain: "O" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 952 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "N" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 662 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 4.91, per 1000 atoms: 0.25 Number of scatterers: 19622 At special positions: 0 Unit cell: (176.64, 151.8, 111.78, 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 67 16.00 P 117 15.00 O 4102 8.00 N 3358 7.00 C 11978 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: 1.83 Conformation dependent library (CDL) restraints added in 829.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 37 sheets defined 26.7% alpha, 22.5% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.773A pdb=" N LYS A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.886A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.580A pdb=" N ARG A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 removed outlier: 4.091A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.715A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.925A pdb=" N ASN A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.727A pdb=" N ASN A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.878A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.530A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.544A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.721A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.562A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.520A pdb=" N VAL C 134 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 removed outlier: 4.659A pdb=" N MET C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.722A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.662A pdb=" N VAL C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.614A pdb=" N ALA C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 111 through 125 removed outlier: 4.507A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 164 through 178 removed outlier: 3.574A pdb=" N GLU D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.506A pdb=" N ILE D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.611A pdb=" N VAL D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 111 through 125 removed outlier: 4.014A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 163 through 178 removed outlier: 4.028A pdb=" N ALA E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.603A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 233 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 284 through 297 Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 111 through 125 removed outlier: 4.505A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE F 123 " --> pdb=" O TYR F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 163 through 178 removed outlier: 3.849A pdb=" N ALA F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 168 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.585A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 278 removed outlier: 3.520A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL F 278 " --> pdb=" O MET F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 111 through 125 removed outlier: 4.425A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 164 through 178 removed outlier: 3.990A pdb=" N GLU G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE G 169 " --> pdb=" O ASP G 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.612A pdb=" N ALA G 232 " --> pdb=" O LYS G 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 233 " --> pdb=" O ILE G 229 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG G 234 " --> pdb=" O GLY G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 279 removed outlier: 3.706A pdb=" N VAL G 278 " --> pdb=" O MET G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 111 through 125 removed outlier: 4.309A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE H 123 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 Processing helix chain 'H' and resid 166 through 178 removed outlier: 4.319A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 removed outlier: 3.627A pdb=" N ALA H 232 " --> pdb=" O LYS H 228 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE H 233 " --> pdb=" O ILE H 229 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG H 234 " --> pdb=" O GLY H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 279 removed outlier: 3.612A pdb=" N VAL H 278 " --> pdb=" O MET H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 3.502A pdb=" N ILE A 32 " --> pdb=" O HIS A 19 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS A 19 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 8.823A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 159 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 161 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 52 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N ASP B 163 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 15.511A pdb=" N VAL B 50 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 97 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 57 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 95 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL B 59 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 93 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 94 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 13 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY B 96 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS B 11 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 98 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 3 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.722A pdb=" N ILE B 126 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS B 11 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 3 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 98 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS B 11 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY B 96 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ASP B 13 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA B 94 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 93 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL B 59 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 95 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE B 57 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 97 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 15.511A pdb=" N VAL B 50 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N ASP B 163 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 52 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 161 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 159 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA B 205 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS B 191 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 207 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 185 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 213 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL B 183 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE B 215 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 removed outlier: 3.793A pdb=" N GLN A 165 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.609A pdb=" N LEU C 77 " --> pdb=" O MET C 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 47 Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 218 Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.700A pdb=" N VAL C 260 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.568A pdb=" N GLY D 299 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 25 current: chain 'D' and resid 140 through 145 Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.651A pdb=" N THR D 35 " --> pdb=" O ALA D 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 77 through 86 current: chain 'D' and resid 217 through 218 Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.543A pdb=" N VAL D 260 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.702A pdb=" N GLY E 299 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 140 through 145 Processing sheet with id=AC2, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.611A pdb=" N THR E 35 " --> pdb=" O ALA E 25 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 86 current: chain 'E' and resid 217 through 218 Processing sheet with id=AC3, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AC4, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.661A pdb=" N VAL E 260 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.766A pdb=" N GLY F 299 " --> pdb=" O TYR F 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC7, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC8, first strand: chain 'F' and resid 41 through 47 Processing sheet with id=AC9, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD1, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.513A pdb=" N GLY G 299 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 140 through 145 Processing sheet with id=AD3, first strand: chain 'G' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 86 current: chain 'G' and resid 217 through 218 Processing sheet with id=AD4, first strand: chain 'G' and resid 41 through 46 Processing sheet with id=AD5, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.554A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'H' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 21 through 26 current: chain 'H' and resid 140 through 144 Processing sheet with id=AD8, first strand: chain 'H' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 86 current: chain 'H' and resid 217 through 218 Processing sheet with id=AD9, first strand: chain 'H' and resid 41 through 47 Processing sheet with id=AE1, first strand: chain 'H' and resid 254 through 255 removed outlier: 3.509A pdb=" N VAL H 260 " --> pdb=" O VAL H 255 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5934 1.34 - 1.46: 4151 1.46 - 1.58: 9787 1.58 - 1.70: 231 1.70 - 1.82: 123 Bond restraints: 20226 Sorted by residual: bond pdb=" CA THR G 244 " pdb=" C THR G 244 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.13e+00 bond pdb=" CA GLU D 108 " pdb=" CB GLU D 108 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CA GLU F 108 " pdb=" CB GLU F 108 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CB GLU H 286 " pdb=" CG GLU H 286 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.63e-01 bond pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.51e-02 4.39e+03 8.28e-01 ... (remaining 20221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 27506 1.88 - 3.76: 410 3.76 - 5.64: 20 5.64 - 7.52: 7 7.52 - 9.39: 3 Bond angle restraints: 27946 Sorted by residual: angle pdb=" C LEU D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C LEU C 107 " pdb=" N GLU C 108 " pdb=" CA GLU C 108 " ideal model delta sigma weight residual 122.61 130.17 -7.56 1.56e+00 4.11e-01 2.35e+01 angle pdb=" C LEU F 107 " pdb=" N GLU F 108 " pdb=" CA GLU F 108 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N PRO F 246 " pdb=" CA PRO F 246 " pdb=" C PRO F 246 " ideal model delta sigma weight residual 111.33 116.15 -4.82 1.43e+00 4.89e-01 1.14e+01 angle pdb=" N PRO E 246 " pdb=" CA PRO E 246 " pdb=" C PRO E 246 " ideal model delta sigma weight residual 111.33 116.00 -4.67 1.43e+00 4.89e-01 1.07e+01 ... (remaining 27941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11356 35.63 - 71.26: 409 71.26 - 106.88: 39 106.88 - 142.51: 1 142.51 - 178.14: 2 Dihedral angle restraints: 11807 sinusoidal: 5427 harmonic: 6380 Sorted by residual: dihedral pdb=" O4' U M 32 " pdb=" C1' U M 32 " pdb=" N1 U M 32 " pdb=" C2 U M 32 " ideal model delta sinusoidal sigma weight residual -128.00 50.14 -178.14 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 3 " pdb=" C1' U M 3 " pdb=" N1 U M 3 " pdb=" C2 U M 3 " ideal model delta sinusoidal sigma weight residual -128.00 48.57 -176.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -99.63 -60.37 1 1.50e+01 4.44e-03 2.16e+01 ... (remaining 11804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2405 0.039 - 0.077: 603 0.077 - 0.116: 153 0.116 - 0.155: 32 0.155 - 0.193: 4 Chirality restraints: 3197 Sorted by residual: chirality pdb=" CB THR F 268 " pdb=" CA THR F 268 " pdb=" OG1 THR F 268 " pdb=" CG2 THR F 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB THR D 268 " pdb=" CA THR D 268 " pdb=" OG1 THR D 268 " pdb=" CG2 THR D 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CB THR G 268 " pdb=" CA THR G 268 " pdb=" OG1 THR G 268 " pdb=" CG2 THR G 268 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 3194 not shown) Planarity restraints: 3231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 239 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.02e+00 pdb=" CG TRP C 239 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 239 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 239 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 239 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 239 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 239 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 239 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 156 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 157 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 159 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C GLU G 159 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU G 159 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE G 160 " 0.009 2.00e-02 2.50e+03 ... (remaining 3228 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1452 2.74 - 3.28: 18514 3.28 - 3.82: 30570 3.82 - 4.36: 36717 4.36 - 4.90: 63982 Nonbonded interactions: 151235 Sorted by model distance: nonbonded pdb=" O ALA H 45 " pdb=" O2' A M 13 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" NE2 GLN F 227 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR H 117 " pdb=" O ASP H 161 " model vdw 2.243 3.040 nonbonded pdb=" O ALA D 45 " pdb=" O2' A M 37 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR F 117 " pdb=" O ASP F 161 " model vdw 2.246 3.040 ... (remaining 151230 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.42 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20226 Z= 0.117 Angle : 0.568 9.395 27946 Z= 0.346 Chirality : 0.038 0.193 3197 Planarity : 0.003 0.042 3231 Dihedral : 16.776 178.140 7733 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.43 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.65 (0.19), residues: 2218 helix: 1.34 (0.25), residues: 485 sheet: 1.37 (0.30), residues: 384 loop : -1.78 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 133 TYR 0.019 0.001 TYR D 240 PHE 0.021 0.001 PHE E 90 TRP 0.034 0.001 TRP C 239 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00212 (20226) covalent geometry : angle 0.56765 (27946) hydrogen bonds : bond 0.17787 ( 620) hydrogen bonds : angle 6.54922 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7232 (mt) cc_final: 0.6989 (mt) REVERT: B 235 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7250 (tp30) REVERT: B 236 ASN cc_start: 0.6617 (t0) cc_final: 0.6350 (t0) REVERT: D 191 MET cc_start: 0.7019 (mpp) cc_final: 0.6778 (mmm) REVERT: F 91 LYS cc_start: 0.7728 (tttp) cc_final: 0.7450 (tmtt) REVERT: G 182 PHE cc_start: 0.7848 (p90) cc_final: 0.7641 (p90) REVERT: G 188 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6976 (mt-10) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1256 time to fit residues: 61.6289 Evaluate side-chains 234 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 279 ASN E 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132929 restraints weight = 29456.726| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.49 r_work: 0.3288 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20226 Z= 0.134 Angle : 0.548 9.088 27946 Z= 0.303 Chirality : 0.040 0.143 3197 Planarity : 0.003 0.039 3231 Dihedral : 17.842 177.563 3843 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.02 % Favored : 90.89 % Rotamer: Outliers : 1.09 % Allowed : 6.96 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.58 (0.19), residues: 2218 helix: 1.37 (0.24), residues: 498 sheet: 1.20 (0.30), residues: 402 loop : -1.72 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 263 TYR 0.019 0.001 TYR D 240 PHE 0.017 0.001 PHE B 202 TRP 0.017 0.001 TRP C 239 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00293 (20226) covalent geometry : angle 0.54789 (27946) hydrogen bonds : bond 0.04564 ( 620) hydrogen bonds : angle 4.16984 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: B 236 ASN cc_start: 0.7027 (t0) cc_final: 0.6610 (t0) REVERT: C 273 LEU cc_start: 0.7976 (mp) cc_final: 0.7776 (mt) REVERT: G 188 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 207 GLU cc_start: 0.6741 (tp30) cc_final: 0.6522 (tp30) outliers start: 20 outliers final: 13 residues processed: 255 average time/residue: 0.1278 time to fit residues: 52.2754 Evaluate side-chains 232 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 90 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 147 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 279 ASN E 214 GLN H 20 ASN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.174464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134676 restraints weight = 33808.801| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.79 r_work: 0.3266 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20226 Z= 0.113 Angle : 0.519 8.195 27946 Z= 0.288 Chirality : 0.039 0.198 3197 Planarity : 0.003 0.039 3231 Dihedral : 17.895 178.654 3843 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.39 % Favored : 91.43 % Rotamer: Outliers : 1.41 % Allowed : 9.19 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.48 (0.19), residues: 2218 helix: 1.55 (0.23), residues: 494 sheet: 1.34 (0.30), residues: 383 loop : -1.68 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 263 TYR 0.019 0.001 TYR D 240 PHE 0.020 0.001 PHE H 205 TRP 0.013 0.001 TRP C 239 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00241 (20226) covalent geometry : angle 0.51948 (27946) hydrogen bonds : bond 0.03955 ( 620) hydrogen bonds : angle 3.82677 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.741 Fit side-chains REVERT: A 7 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: A 174 GLU cc_start: 0.7377 (pp20) cc_final: 0.6663 (tm-30) REVERT: B 48 LYS cc_start: 0.7652 (mmmt) cc_final: 0.6915 (mtpp) REVERT: B 103 GLU cc_start: 0.5866 (tm-30) cc_final: 0.5557 (tm-30) REVERT: B 115 ASP cc_start: 0.8166 (t0) cc_final: 0.7961 (t0) REVERT: B 182 MET cc_start: 0.7788 (ttt) cc_final: 0.7324 (ttt) REVERT: B 236 ASN cc_start: 0.7213 (t0) cc_final: 0.6803 (t0) REVERT: C 214 GLN cc_start: 0.6002 (pt0) cc_final: 0.5754 (pm20) REVERT: C 289 MET cc_start: 0.5770 (mmp) cc_final: 0.5470 (mtt) REVERT: D 38 MET cc_start: 0.7926 (mmp) cc_final: 0.7679 (mmp) REVERT: G 188 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7966 (mt-10) outliers start: 26 outliers final: 17 residues processed: 274 average time/residue: 0.1343 time to fit residues: 58.8565 Evaluate side-chains 245 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 51 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 201 optimal weight: 0.3980 overall best weight: 0.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 78 ASN C 27 ASN C 146 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN H 294 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133162 restraints weight = 35583.993| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.92 r_work: 0.3261 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20226 Z= 0.109 Angle : 0.504 6.155 27946 Z= 0.281 Chirality : 0.039 0.165 3197 Planarity : 0.003 0.037 3231 Dihedral : 17.883 178.690 3843 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.57 % Favored : 91.29 % Rotamer: Outliers : 2.07 % Allowed : 10.06 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.37 (0.19), residues: 2218 helix: 1.77 (0.24), residues: 476 sheet: 1.19 (0.30), residues: 384 loop : -1.54 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 263 TYR 0.016 0.001 TYR D 240 PHE 0.018 0.001 PHE B 202 TRP 0.016 0.001 TRP G 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00231 (20226) covalent geometry : angle 0.50429 (27946) hydrogen bonds : bond 0.03779 ( 620) hydrogen bonds : angle 3.72381 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 48 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7360 (mtpp) REVERT: B 103 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5539 (tm-30) REVERT: B 115 ASP cc_start: 0.8077 (t0) cc_final: 0.7825 (t0) REVERT: B 151 VAL cc_start: 0.6838 (p) cc_final: 0.6603 (p) REVERT: B 182 MET cc_start: 0.7793 (ttt) cc_final: 0.7306 (ttt) REVERT: C 214 GLN cc_start: 0.6044 (pt0) cc_final: 0.5769 (pm20) REVERT: D 38 MET cc_start: 0.7744 (mmp) cc_final: 0.7444 (mmp) REVERT: G 188 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7830 (mt-10) REVERT: H 275 ASP cc_start: 0.7662 (m-30) cc_final: 0.7286 (m-30) outliers start: 38 outliers final: 26 residues processed: 269 average time/residue: 0.1319 time to fit residues: 56.9795 Evaluate side-chains 261 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 92 optimal weight: 0.0020 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 189 optimal weight: 0.0570 chunk 137 optimal weight: 0.2980 chunk 230 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 206 optimal weight: 0.0670 chunk 196 optimal weight: 0.0970 chunk 111 optimal weight: 7.9990 overall best weight: 0.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 294 ASN H 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.178805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140405 restraints weight = 28013.226| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.57 r_work: 0.3375 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20226 Z= 0.100 Angle : 0.493 10.048 27946 Z= 0.273 Chirality : 0.038 0.160 3197 Planarity : 0.003 0.038 3231 Dihedral : 17.864 178.672 3843 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.84 % Rotamer: Outliers : 1.63 % Allowed : 11.36 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.24 (0.19), residues: 2218 helix: 1.92 (0.24), residues: 476 sheet: 0.91 (0.27), residues: 468 loop : -1.50 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 133 TYR 0.018 0.001 TYR G 240 PHE 0.022 0.001 PHE B 202 TRP 0.015 0.001 TRP G 130 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00202 (20226) covalent geometry : angle 0.49263 (27946) hydrogen bonds : bond 0.03566 ( 620) hydrogen bonds : angle 3.50109 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 10 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7805 (pt) REVERT: B 40 SER cc_start: 0.7820 (t) cc_final: 0.7428 (p) REVERT: B 182 MET cc_start: 0.7818 (ttt) cc_final: 0.7346 (ttt) REVERT: D 38 MET cc_start: 0.7717 (mmp) cc_final: 0.7354 (mmp) REVERT: D 210 LYS cc_start: 0.8078 (mttp) cc_final: 0.7853 (mmmt) REVERT: F 108 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.4615 (mt-10) REVERT: G 188 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7690 (mt-10) REVERT: G 211 LEU cc_start: 0.9063 (mp) cc_final: 0.8732 (mt) outliers start: 30 outliers final: 17 residues processed: 278 average time/residue: 0.1322 time to fit residues: 59.0960 Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 4 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN B 78 ASN C 17 ASN D 17 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN H 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.160919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117714 restraints weight = 26078.400| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.51 r_work: 0.3036 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 20226 Z= 0.378 Angle : 0.795 14.230 27946 Z= 0.433 Chirality : 0.051 0.232 3197 Planarity : 0.006 0.061 3231 Dihedral : 18.130 179.562 3843 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.78 % Favored : 88.81 % Rotamer: Outliers : 2.88 % Allowed : 11.80 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -1.20 (0.18), residues: 2218 helix: 0.62 (0.23), residues: 503 sheet: 0.72 (0.29), residues: 384 loop : -1.96 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 257 TYR 0.018 0.003 TYR C 240 PHE 0.059 0.003 PHE H 205 TRP 0.022 0.003 TRP E 130 HIS 0.009 0.003 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00886 (20226) covalent geometry : angle 0.79507 (27946) hydrogen bonds : bond 0.06168 ( 620) hydrogen bonds : angle 4.56434 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 10 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7840 (pt) REVERT: A 174 GLU cc_start: 0.7646 (pp20) cc_final: 0.6806 (tm-30) REVERT: B 26 MET cc_start: 0.8171 (mmm) cc_final: 0.7865 (tpt) REVERT: B 37 GLU cc_start: 0.7858 (tp30) cc_final: 0.7532 (tp30) REVERT: B 75 ASP cc_start: 0.8596 (p0) cc_final: 0.8247 (p0) REVERT: B 219 MET cc_start: 0.7291 (tpt) cc_final: 0.7046 (tpt) REVERT: C 88 ASP cc_start: 0.6954 (m-30) cc_final: 0.6744 (t0) REVERT: D 210 LYS cc_start: 0.8175 (mttp) cc_final: 0.7930 (mmmt) REVERT: G 109 ASN cc_start: 0.8148 (t0) cc_final: 0.7715 (t0) REVERT: G 132 ASN cc_start: 0.9043 (OUTLIER) cc_final: 0.8784 (m110) REVERT: G 188 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7904 (mt-10) REVERT: H 207 GLU cc_start: 0.7292 (tp30) cc_final: 0.6955 (tp30) outliers start: 53 outliers final: 38 residues processed: 269 average time/residue: 0.1401 time to fit residues: 59.8269 Evaluate side-chains 254 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 223 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 162 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129959 restraints weight = 27230.393| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.39 r_work: 0.3204 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20226 Z= 0.119 Angle : 0.559 10.904 27946 Z= 0.307 Chirality : 0.040 0.170 3197 Planarity : 0.004 0.041 3231 Dihedral : 17.969 176.057 3843 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.39 % Favored : 91.38 % Rotamer: Outliers : 2.12 % Allowed : 13.54 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.76 (0.18), residues: 2218 helix: 1.28 (0.23), residues: 486 sheet: 0.55 (0.28), residues: 425 loop : -1.67 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 234 TYR 0.033 0.001 TYR A 86 PHE 0.019 0.001 PHE H 205 TRP 0.017 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00250 (20226) covalent geometry : angle 0.55876 (27946) hydrogen bonds : bond 0.03780 ( 620) hydrogen bonds : angle 3.94781 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: A 10 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7788 (pt) REVERT: B 26 MET cc_start: 0.7976 (mmm) cc_final: 0.7689 (tpt) REVERT: B 37 GLU cc_start: 0.7467 (tp30) cc_final: 0.7236 (tp30) REVERT: B 219 MET cc_start: 0.6658 (tpt) cc_final: 0.6443 (tpt) REVERT: C 88 ASP cc_start: 0.7005 (m-30) cc_final: 0.6762 (t0) REVERT: C 191 MET cc_start: 0.7366 (mtm) cc_final: 0.6687 (mtp) REVERT: D 38 MET cc_start: 0.7848 (mmp) cc_final: 0.7466 (mmp) REVERT: D 210 LYS cc_start: 0.8099 (mttp) cc_final: 0.7862 (mmmt) REVERT: F 108 GLU cc_start: 0.5108 (OUTLIER) cc_final: 0.3930 (mt-10) REVERT: G 109 ASN cc_start: 0.7980 (t0) cc_final: 0.7484 (t0) REVERT: G 132 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7576 (m-40) REVERT: G 188 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7920 (mt-10) REVERT: H 207 GLU cc_start: 0.7108 (tp30) cc_final: 0.6826 (tp30) outliers start: 39 outliers final: 27 residues processed: 252 average time/residue: 0.1204 time to fit residues: 49.6505 Evaluate side-chains 252 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 160 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 0.0980 chunk 158 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129000 restraints weight = 33547.945| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.82 r_work: 0.3188 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20226 Z= 0.121 Angle : 0.555 10.475 27946 Z= 0.303 Chirality : 0.040 0.160 3197 Planarity : 0.004 0.040 3231 Dihedral : 17.926 178.149 3843 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.29 % Favored : 90.53 % Rotamer: Outliers : 2.01 % Allowed : 14.25 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.64 (0.18), residues: 2218 helix: 1.43 (0.23), residues: 484 sheet: 0.61 (0.27), residues: 455 loop : -1.65 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 133 TYR 0.028 0.001 TYR A 86 PHE 0.023 0.001 PHE B 202 TRP 0.014 0.001 TRP F 130 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00260 (20226) covalent geometry : angle 0.55489 (27946) hydrogen bonds : bond 0.03693 ( 620) hydrogen bonds : angle 3.78989 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 10 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7728 (pt) REVERT: B 26 MET cc_start: 0.7965 (mmm) cc_final: 0.7682 (tpt) REVERT: B 115 ASP cc_start: 0.7952 (t0) cc_final: 0.7605 (t0) REVERT: B 198 MET cc_start: 0.8396 (mmm) cc_final: 0.8134 (mmm) REVERT: B 219 MET cc_start: 0.6741 (tpt) cc_final: 0.6504 (tpt) REVERT: C 88 ASP cc_start: 0.7033 (m-30) cc_final: 0.6830 (t0) REVERT: C 191 MET cc_start: 0.7403 (mtm) cc_final: 0.6725 (mtp) REVERT: D 38 MET cc_start: 0.7847 (mmp) cc_final: 0.7479 (mmp) REVERT: D 294 ASN cc_start: 0.7700 (t0) cc_final: 0.7400 (t0) REVERT: F 108 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.3983 (mt-10) REVERT: G 109 ASN cc_start: 0.7920 (t0) cc_final: 0.7438 (t0) REVERT: G 132 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7443 (m-40) REVERT: G 188 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7970 (mt-10) outliers start: 37 outliers final: 29 residues processed: 252 average time/residue: 0.1260 time to fit residues: 51.9008 Evaluate side-chains 249 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 156 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.166684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124001 restraints weight = 29738.090| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.76 r_work: 0.3103 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20226 Z= 0.182 Angle : 0.612 10.964 27946 Z= 0.335 Chirality : 0.042 0.209 3197 Planarity : 0.004 0.044 3231 Dihedral : 17.963 179.170 3843 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.24 % Favored : 89.49 % Rotamer: Outliers : 2.12 % Allowed : 14.14 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.76 (0.18), residues: 2218 helix: 1.30 (0.23), residues: 486 sheet: 0.52 (0.27), residues: 425 loop : -1.66 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 133 TYR 0.029 0.002 TYR A 86 PHE 0.026 0.002 PHE H 205 TRP 0.013 0.002 TRP C 239 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00418 (20226) covalent geometry : angle 0.61244 (27946) hydrogen bonds : bond 0.04257 ( 620) hydrogen bonds : angle 4.00008 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 10 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7716 (pt) REVERT: B 26 MET cc_start: 0.8040 (mmm) cc_final: 0.7749 (tpt) REVERT: B 37 GLU cc_start: 0.7770 (tp30) cc_final: 0.7490 (tp30) REVERT: B 219 MET cc_start: 0.6964 (tpt) cc_final: 0.6754 (tpt) REVERT: C 88 ASP cc_start: 0.7028 (m-30) cc_final: 0.6804 (t0) REVERT: C 191 MET cc_start: 0.7420 (mtm) cc_final: 0.6796 (mtp) REVERT: C 294 ASN cc_start: 0.7668 (m-40) cc_final: 0.7324 (m-40) REVERT: D 93 GLU cc_start: 0.6998 (pt0) cc_final: 0.6778 (pt0) REVERT: F 108 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.3987 (mt-10) REVERT: G 109 ASN cc_start: 0.8046 (t0) cc_final: 0.7582 (t0) REVERT: G 188 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7995 (mt-10) REVERT: G 207 GLU cc_start: 0.7530 (mp0) cc_final: 0.6626 (mm-30) REVERT: H 250 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7813 (mt-10) outliers start: 39 outliers final: 33 residues processed: 245 average time/residue: 0.1235 time to fit residues: 48.8281 Evaluate side-chains 248 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 74 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 138 optimal weight: 0.0980 chunk 23 optimal weight: 0.4980 chunk 161 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129073 restraints weight = 35559.964| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.96 r_work: 0.3198 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20226 Z= 0.113 Angle : 0.550 9.845 27946 Z= 0.302 Chirality : 0.040 0.166 3197 Planarity : 0.003 0.041 3231 Dihedral : 17.921 177.660 3843 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.80 % Favored : 91.02 % Rotamer: Outliers : 1.85 % Allowed : 14.68 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.61 (0.19), residues: 2218 helix: 1.50 (0.24), residues: 486 sheet: 0.51 (0.26), residues: 467 loop : -1.62 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 234 TYR 0.031 0.001 TYR A 86 PHE 0.024 0.001 PHE B 202 TRP 0.016 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00238 (20226) covalent geometry : angle 0.55010 (27946) hydrogen bonds : bond 0.03588 ( 620) hydrogen bonds : angle 3.77059 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 10 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7678 (pt) REVERT: B 115 ASP cc_start: 0.7959 (t0) cc_final: 0.7587 (t0) REVERT: B 198 MET cc_start: 0.8396 (mmm) cc_final: 0.8165 (mmm) REVERT: B 219 MET cc_start: 0.6691 (tpt) cc_final: 0.6465 (tpt) REVERT: C 88 ASP cc_start: 0.7120 (m-30) cc_final: 0.6863 (t0) REVERT: C 191 MET cc_start: 0.7347 (mtm) cc_final: 0.6777 (mtp) REVERT: C 294 ASN cc_start: 0.7567 (m-40) cc_final: 0.7282 (m-40) REVERT: D 274 MET cc_start: 0.8165 (mtp) cc_final: 0.7930 (mtp) REVERT: F 108 GLU cc_start: 0.5189 (OUTLIER) cc_final: 0.3979 (mt-10) REVERT: G 109 ASN cc_start: 0.7974 (t0) cc_final: 0.7495 (t0) REVERT: G 163 ASP cc_start: 0.7639 (t70) cc_final: 0.7358 (t0) REVERT: G 188 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 191 MET cc_start: 0.7926 (mmm) cc_final: 0.7563 (mtm) REVERT: G 207 GLU cc_start: 0.7504 (mp0) cc_final: 0.6635 (mm-30) REVERT: H 250 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7722 (mt-10) outliers start: 34 outliers final: 27 residues processed: 254 average time/residue: 0.1228 time to fit residues: 50.7645 Evaluate side-chains 255 residues out of total 1849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 94 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128266 restraints weight = 27386.269| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.49 r_work: 0.3213 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20226 Z= 0.125 Angle : 0.558 9.939 27946 Z= 0.305 Chirality : 0.040 0.161 3197 Planarity : 0.003 0.040 3231 Dihedral : 17.901 179.222 3843 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.21 % Rotamer: Outliers : 1.85 % Allowed : 14.85 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 aren not related in a simple way. whole: -0.57 (0.19), residues: 2218 helix: 1.56 (0.24), residues: 486 sheet: 0.58 (0.26), residues: 455 loop : -1.62 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 133 TYR 0.032 0.001 TYR A 86 PHE 0.025 0.001 PHE B 202 TRP 0.015 0.001 TRP C 239 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00274 (20226) covalent geometry : angle 0.55792 (27946) hydrogen bonds : bond 0.03636 ( 620) hydrogen bonds : angle 3.75414 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5211.11 seconds wall clock time: 89 minutes 40.11 seconds (5380.11 seconds total)