Starting phenix.real_space_refine on Sun Sep 29 09:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_32874.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_32874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_32874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_32874.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwv_32874/09_2024/7wwv_32874.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 12.29, per 1000 atoms: 0.63 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: 4.53 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 6.55 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: 5.92 Time building geometry restraints manager: 5.32 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 47.010 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.610 ------------------------------------------------------------------------------- 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= 0.134 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 : 6.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.001 TRP C 239 HIS 0.002 0.001 HIS E 189 PHE 0.021 0.001 PHE E 90 TYR 0.019 0.001 TYR D 240 ARG 0.003 0.000 ARG F 133 *********************** 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 fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.895 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: 0.2725 time to fit residues: 131.8603 Evaluate side-chains 234 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN B 74 GLN C 279 ASN D 17 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 20 ASN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20226 Z= 0.295 Angle : 0.627 11.347 27946 Z= 0.344 Chirality : 0.043 0.178 3197 Planarity : 0.004 0.044 3231 Dihedral : 18.107 178.023 3843 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.74 % Favored : 90.03 % Rotamer: Outliers : 1.14 % Allowed : 7.88 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2218 helix: 1.11 (0.23), residues: 497 sheet: 1.07 (0.30), residues: 402 loop : -1.80 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 239 HIS 0.006 0.002 HIS E 189 PHE 0.024 0.002 PHE H 205 TYR 0.016 0.002 TYR D 240 ARG 0.006 0.001 ARG E 14 *********************** 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 257 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 1.831 Fit side-chains REVERT: B 236 ASN cc_start: 0.6910 (t0) cc_final: 0.6617 (t0) REVERT: C 38 MET cc_start: 0.5879 (mmm) cc_final: 0.5677 (mmm) REVERT: G 109 ASN cc_start: 0.7435 (t0) cc_final: 0.7121 (t0) REVERT: G 188 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7336 (mt-10) REVERT: H 172 MET cc_start: 0.7563 (mtp) cc_final: 0.7173 (mtp) REVERT: H 207 GLU cc_start: 0.6524 (tp30) cc_final: 0.6307 (tp30) REVERT: H 274 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8026 (mtp) outliers start: 21 outliers final: 16 residues processed: 252 average time/residue: 0.2857 time to fit residues: 113.9703 Evaluate side-chains 232 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 156 LEU 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 274 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN C 17 ASN C 279 ASN E 17 ASN E 53 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20226 Z= 0.213 Angle : 0.560 9.411 27946 Z= 0.311 Chirality : 0.041 0.194 3197 Planarity : 0.004 0.040 3231 Dihedral : 18.009 179.889 3843 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.25 % Favored : 90.53 % Rotamer: Outliers : 1.69 % Allowed : 10.39 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2218 helix: 1.21 (0.23), residues: 500 sheet: 0.92 (0.29), residues: 414 loop : -1.79 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 130 HIS 0.003 0.001 HIS D 225 PHE 0.027 0.002 PHE H 205 TYR 0.016 0.001 TYR D 240 ARG 0.003 0.000 ARG A 22 *********************** 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 273 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.994 Fit side-chains REVERT: A 7 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 10 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7917 (pt) REVERT: A 174 GLU cc_start: 0.7144 (pp20) cc_final: 0.6424 (tm-30) REVERT: B 182 MET cc_start: 0.6940 (ttt) cc_final: 0.6694 (ttt) REVERT: B 219 MET cc_start: 0.6782 (tpt) cc_final: 0.6500 (tpt) REVERT: C 191 MET cc_start: 0.6965 (mtm) cc_final: 0.6335 (mtp) REVERT: D 38 MET cc_start: 0.7245 (mmp) cc_final: 0.6987 (mmp) REVERT: E 249 VAL cc_start: 0.8929 (m) cc_final: 0.8689 (m) REVERT: E 289 MET cc_start: 0.8140 (mtm) cc_final: 0.7913 (mtp) REVERT: G 109 ASN cc_start: 0.7514 (t0) cc_final: 0.7143 (t0) REVERT: G 188 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7215 (mt-10) REVERT: H 172 MET cc_start: 0.7639 (mtp) cc_final: 0.7302 (mtp) REVERT: H 250 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6812 (mt-10) REVERT: H 274 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8135 (mtp) outliers start: 31 outliers final: 24 residues processed: 263 average time/residue: 0.2815 time to fit residues: 116.7668 Evaluate side-chains 249 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 2.073 ------------------------------------------------------------------------------- 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 131 LEU 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 168 GLU 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 197 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 156 LEU 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 G residue 247 ILE 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 274 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 5.9990 chunk 158 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 0.0060 chunk 60 optimal weight: 0.4980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 ASN H 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1891 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= 0.153 Angle : 0.535 9.330 27946 Z= 0.296 Chirality : 0.040 0.173 3197 Planarity : 0.003 0.038 3231 Dihedral : 17.976 179.133 3843 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.16 % Favored : 90.66 % Rotamer: Outliers : 2.28 % Allowed : 11.20 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2218 helix: 1.34 (0.23), residues: 501 sheet: 0.93 (0.29), residues: 414 loop : -1.74 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 130 HIS 0.002 0.001 HIS F 189 PHE 0.017 0.001 PHE B 202 TYR 0.016 0.001 TYR G 240 ARG 0.005 0.000 ARG F 133 *********************** 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 285 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: A 10 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7758 (pt) REVERT: A 174 GLU cc_start: 0.7106 (pp20) cc_final: 0.6426 (tm-30) REVERT: B 151 VAL cc_start: 0.6932 (p) cc_final: 0.6662 (p) REVERT: B 219 MET cc_start: 0.6591 (tpt) cc_final: 0.6391 (tpt) REVERT: C 73 ASN cc_start: 0.4850 (p0) cc_final: 0.4613 (p0) REVERT: C 191 MET cc_start: 0.6748 (mtm) cc_final: 0.6386 (mtp) REVERT: D 38 MET cc_start: 0.7254 (mmp) cc_final: 0.6929 (mmp) REVERT: G 109 ASN cc_start: 0.7374 (t0) cc_final: 0.6993 (t0) REVERT: G 188 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7185 (mt-10) REVERT: H 172 MET cc_start: 0.7718 (mtp) cc_final: 0.7388 (mtp) REVERT: H 205 PHE cc_start: 0.7713 (t80) cc_final: 0.7316 (t80) REVERT: H 250 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6769 (mt-10) REVERT: H 274 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8050 (mtp) outliers start: 42 outliers final: 24 residues processed: 268 average time/residue: 0.2754 time to fit residues: 117.4796 Evaluate side-chains 247 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 168 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 156 LEU 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 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 Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 166 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 ASN F 294 ASN G 132 ASN H 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20226 Z= 0.279 Angle : 0.598 8.024 27946 Z= 0.331 Chirality : 0.042 0.227 3197 Planarity : 0.004 0.040 3231 Dihedral : 17.988 179.767 3843 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.97 % Favored : 89.81 % Rotamer: Outliers : 2.77 % Allowed : 12.23 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2218 helix: 1.20 (0.23), residues: 502 sheet: 0.90 (0.29), residues: 384 loop : -1.81 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 130 HIS 0.004 0.001 HIS E 189 PHE 0.020 0.002 PHE B 202 TYR 0.014 0.002 TYR C 240 ARG 0.005 0.000 ARG C 234 *********************** 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 280 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 10 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7794 (pt) REVERT: A 58 GLU cc_start: 0.7154 (tt0) cc_final: 0.6939 (pm20) REVERT: A 174 GLU cc_start: 0.7109 (pp20) cc_final: 0.6432 (tm-30) REVERT: B 151 VAL cc_start: 0.7001 (p) cc_final: 0.6732 (p) REVERT: C 73 ASN cc_start: 0.4878 (p0) cc_final: 0.4630 (p0) REVERT: E 300 VAL cc_start: 0.8390 (OUTLIER) cc_final: 0.8027 (p) REVERT: G 109 ASN cc_start: 0.7575 (t0) cc_final: 0.7200 (t0) REVERT: G 188 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7246 (mt-10) REVERT: H 172 MET cc_start: 0.7714 (mtp) cc_final: 0.7367 (mtp) REVERT: H 207 GLU cc_start: 0.6595 (tp30) cc_final: 0.6390 (tp30) REVERT: H 274 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8038 (mtp) outliers start: 51 outliers final: 41 residues processed: 262 average time/residue: 0.2715 time to fit residues: 112.8952 Evaluate side-chains 263 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 1.821 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 147 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 176 VAL 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 145 VAL Chi-restraints excluded: chain F residue 156 LEU 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 187 VAL Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 MET 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 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 289 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20226 Z= 0.347 Angle : 0.646 8.945 27946 Z= 0.356 Chirality : 0.044 0.227 3197 Planarity : 0.004 0.044 3231 Dihedral : 18.021 178.712 3843 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.28 % Favored : 89.40 % Rotamer: Outliers : 3.10 % Allowed : 12.89 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2218 helix: 0.85 (0.23), residues: 502 sheet: 0.44 (0.28), residues: 425 loop : -1.90 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 239 HIS 0.006 0.002 HIS D 225 PHE 0.023 0.002 PHE B 202 TYR 0.015 0.002 TYR C 240 ARG 0.006 0.001 ARG C 234 *********************** 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 283 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: A 10 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7780 (pt) REVERT: A 174 GLU cc_start: 0.7205 (pp20) cc_final: 0.6536 (tm-30) REVERT: B 37 GLU cc_start: 0.7579 (tp30) cc_final: 0.7377 (tp30) REVERT: B 151 VAL cc_start: 0.7055 (p) cc_final: 0.6787 (p) REVERT: C 73 ASN cc_start: 0.5027 (p0) cc_final: 0.4728 (p0) REVERT: G 109 ASN cc_start: 0.7676 (t0) cc_final: 0.7293 (t0) REVERT: G 188 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7251 (mt-10) REVERT: G 207 GLU cc_start: 0.7091 (mp0) cc_final: 0.6531 (mm-30) REVERT: H 207 GLU cc_start: 0.6779 (tp30) cc_final: 0.6534 (tp30) REVERT: H 274 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: H 294 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8265 (t0) outliers start: 57 outliers final: 46 residues processed: 268 average time/residue: 0.2978 time to fit residues: 125.1644 Evaluate side-chains 260 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 101 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 101 CYS 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 168 GLU 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 107 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER 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 145 VAL Chi-restraints excluded: chain F residue 156 LEU 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 27 ASN 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 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 MET Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain H residue 294 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN F 109 ASN H 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20226 Z= 0.196 Angle : 0.573 9.632 27946 Z= 0.316 Chirality : 0.041 0.213 3197 Planarity : 0.004 0.046 3231 Dihedral : 17.981 177.247 3843 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.65 % Favored : 90.17 % Rotamer: Outliers : 2.99 % Allowed : 13.32 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2218 helix: 1.10 (0.23), residues: 501 sheet: 0.49 (0.28), residues: 425 loop : -1.83 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 130 HIS 0.004 0.001 HIS E 72 PHE 0.018 0.001 PHE B 202 TYR 0.016 0.001 TYR G 240 ARG 0.011 0.000 ARG C 234 *********************** 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 278 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 223 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: A 10 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7735 (pt) REVERT: A 174 GLU cc_start: 0.7165 (pp20) cc_final: 0.6530 (tm-30) REVERT: B 151 VAL cc_start: 0.7015 (p) cc_final: 0.6724 (p) REVERT: E 289 MET cc_start: 0.8198 (mtm) cc_final: 0.7921 (mtp) REVERT: F 108 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.3964 (mt-10) REVERT: G 109 ASN cc_start: 0.7616 (t0) cc_final: 0.7202 (t0) REVERT: G 188 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7214 (mt-10) REVERT: G 207 GLU cc_start: 0.7047 (mp0) cc_final: 0.6498 (mm-30) REVERT: H 172 MET cc_start: 0.7712 (mtp) cc_final: 0.7357 (mtp) REVERT: H 274 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8178 (mtp) outliers start: 55 outliers final: 42 residues processed: 265 average time/residue: 0.3304 time to fit residues: 142.9236 Evaluate side-chains 259 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 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 168 GLU 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 109 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 294 ASN 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 156 LEU 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 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20226 Z= 0.259 Angle : 0.605 8.642 27946 Z= 0.332 Chirality : 0.042 0.247 3197 Planarity : 0.004 0.045 3231 Dihedral : 17.985 178.332 3843 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.06 % Favored : 89.72 % Rotamer: Outliers : 3.15 % Allowed : 13.70 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2218 helix: 1.03 (0.23), residues: 502 sheet: 0.53 (0.28), residues: 410 loop : -1.86 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 239 HIS 0.004 0.001 HIS F 189 PHE 0.023 0.002 PHE B 202 TYR 0.014 0.002 TYR C 240 ARG 0.009 0.000 ARG F 133 *********************** 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 274 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 216 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 10 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7739 (pt) REVERT: A 174 GLU cc_start: 0.7120 (pp20) cc_final: 0.6508 (tm-30) REVERT: B 151 VAL cc_start: 0.6980 (p) cc_final: 0.6720 (p) REVERT: B 219 MET cc_start: 0.7004 (tpt) cc_final: 0.6765 (tpt) REVERT: E 289 MET cc_start: 0.8213 (mtm) cc_final: 0.7941 (mtp) REVERT: F 108 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.4011 (mt-10) REVERT: G 109 ASN cc_start: 0.7636 (t0) cc_final: 0.7229 (t0) REVERT: G 188 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7244 (mt-10) REVERT: G 207 GLU cc_start: 0.7038 (mp0) cc_final: 0.6511 (mm-30) REVERT: H 172 MET cc_start: 0.7745 (mtp) cc_final: 0.7392 (mtp) REVERT: H 274 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: H 294 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8158 (t0) outliers start: 58 outliers final: 46 residues processed: 261 average time/residue: 0.2725 time to fit residues: 113.5750 Evaluate side-chains 263 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain B residue 7 VAL 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 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 168 GLU 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 107 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU 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 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 199 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 274 MET Chi-restraints excluded: chain H residue 289 MET Chi-restraints excluded: chain H residue 294 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.0070 chunk 162 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 overall best weight: 1.3202 ------------------------------------------------------------------------------- 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** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20226 Z= 0.212 Angle : 0.585 11.248 27946 Z= 0.320 Chirality : 0.041 0.225 3197 Planarity : 0.004 0.042 3231 Dihedral : 17.972 178.073 3843 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.88 % Favored : 89.94 % Rotamer: Outliers : 2.88 % Allowed : 14.36 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2218 helix: 1.32 (0.24), residues: 483 sheet: 0.55 (0.28), residues: 410 loop : -1.75 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 130 HIS 0.004 0.001 HIS E 72 PHE 0.024 0.001 PHE B 202 TYR 0.017 0.001 TYR G 240 ARG 0.009 0.000 ARG C 234 *********************** 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 268 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 10 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7644 (pt) REVERT: A 174 GLU cc_start: 0.7087 (pp20) cc_final: 0.6500 (tm-30) REVERT: B 151 VAL cc_start: 0.6953 (p) cc_final: 0.6707 (p) REVERT: B 219 MET cc_start: 0.6755 (tpt) cc_final: 0.6440 (tpt) REVERT: D 191 MET cc_start: 0.7691 (mpp) cc_final: 0.7394 (mmm) REVERT: E 289 MET cc_start: 0.8212 (mtm) cc_final: 0.7941 (mtp) REVERT: F 108 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.3983 (mt-10) REVERT: G 109 ASN cc_start: 0.7612 (t0) cc_final: 0.7204 (t0) REVERT: G 188 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7238 (mt-10) REVERT: G 207 GLU cc_start: 0.7100 (mp0) cc_final: 0.6547 (mm-30) REVERT: H 172 MET cc_start: 0.7722 (mtp) cc_final: 0.7363 (mtp) REVERT: H 274 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8199 (mtp) outliers start: 53 outliers final: 47 residues processed: 255 average time/residue: 0.2702 time to fit residues: 110.3110 Evaluate side-chains 260 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 209 time to evaluate : 1.955 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 66 THR 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 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 168 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU 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 27 ASN 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 247 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 199 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 274 MET 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 219 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN H 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2585 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= 0.161 Angle : 0.562 10.160 27946 Z= 0.308 Chirality : 0.040 0.197 3197 Planarity : 0.004 0.049 3231 Dihedral : 17.926 178.226 3843 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.47 % Favored : 90.35 % Rotamer: Outliers : 2.39 % Allowed : 15.06 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 2218 helix: 1.34 (0.23), residues: 501 sheet: 0.40 (0.26), residues: 470 loop : -1.78 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 130 HIS 0.004 0.001 HIS E 72 PHE 0.026 0.001 PHE B 202 TYR 0.017 0.001 TYR G 240 ARG 0.009 0.000 ARG F 133 ********************** 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 271 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 227 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 10 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7603 (pt) REVERT: A 174 GLU cc_start: 0.7054 (pp20) cc_final: 0.6480 (tm-30) REVERT: B 151 VAL cc_start: 0.6900 (p) cc_final: 0.6658 (p) REVERT: B 219 MET cc_start: 0.6653 (tpt) cc_final: 0.6444 (tpt) REVERT: D 191 MET cc_start: 0.7618 (mpp) cc_final: 0.7349 (mmm) REVERT: E 289 MET cc_start: 0.8284 (mtm) cc_final: 0.7992 (mtp) REVERT: F 108 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.4586 (tt0) REVERT: G 109 ASN cc_start: 0.7565 (t0) cc_final: 0.7142 (t0) REVERT: G 188 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7214 (mt-10) REVERT: G 207 GLU cc_start: 0.7096 (mp0) cc_final: 0.6534 (mm-30) REVERT: H 172 MET cc_start: 0.7796 (mtp) cc_final: 0.7456 (mtp) REVERT: H 274 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8158 (mtp) outliers start: 44 outliers final: 37 residues processed: 259 average time/residue: 0.2755 time to fit residues: 114.4649 Evaluate side-chains 256 residues out of total 1849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 215 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 168 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 252 TYR 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 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 284 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 274 MET 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 238 THR Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.0870 chunk 183 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128729 restraints weight = 27581.059| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.38 r_work: 0.3224 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20226 Z= 0.163 Angle : 0.559 10.112 27946 Z= 0.305 Chirality : 0.040 0.175 3197 Planarity : 0.004 0.042 3231 Dihedral : 17.904 179.086 3843 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.52 % Favored : 90.30 % Rotamer: Outliers : 2.45 % Allowed : 15.28 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2218 helix: 1.39 (0.23), residues: 501 sheet: 0.45 (0.27), residues: 470 loop : -1.75 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 130 HIS 0.004 0.001 HIS E 72 PHE 0.025 0.001 PHE B 202 TYR 0.017 0.001 TYR G 240 ARG 0.008 0.000 ARG F 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.64 seconds wall clock time: 69 minutes 52.56 seconds (4192.56 seconds total)