Starting phenix.real_space_refine on Thu Jun 19 06:35:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwu_32873/06_2025/7wwu_32873.cif" } resolution = 3.5 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= 0.005 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 4092 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 49 5.49 5 S 67 5.16 5 C 11635 2.51 5 N 3241 2.21 5 O 3872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18864 Number of models: 1 Model: "" Number of chains: 10 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: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2302 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 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: "I" Number of atoms: 657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 9, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 267 Conformer: "B" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 10, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 9, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 267 bond proxies already assigned to first conformer: 651 Chain: "M" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1015 Classifications: {'DNA': 1, 'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 10, 'rna3p_pyr': 20} Link IDs: {'rna2p': 18, 'rna3p': 31} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan2': 1, ' G%rna3p_pur:plan': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 12.15, per 1000 atoms: 0.64 Number of scatterers: 18864 At special positions: 0 Unit cell: (147.66, 144.9, 118.68, 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 49 15.00 O 3872 8.00 N 3241 7.00 C 11635 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: 4.44 Conformation dependent library (CDL) restraints added in 2.6 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 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: 58 helices and 37 sheets defined 25.1% alpha, 18.0% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.970A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 4.062A pdb=" N VAL A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN A 67 " --> pdb=" O TRP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.014A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.751A pdb=" N LEU A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 4.117A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.020A pdb=" N LYS B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.957A pdb=" N ASP B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.782A pdb=" N GLN B 228 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 4.094A pdb=" N ASP C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 112 through 125 removed outlier: 4.215A pdb=" N ALA C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 178 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 284 through 297 removed outlier: 3.620A pdb=" N ARG C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.680A pdb=" N ASP D 56 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA D 57 " --> pdb=" O PRO D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.932A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.959A pdb=" N ALA D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.570A pdb=" N THR E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.750A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 4.703A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.937A pdb=" N ILE E 229 " --> pdb=" O HIS E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.752A pdb=" N ARG E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 111 through 126 removed outlier: 4.367A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.854A 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 166 through 177 removed outlier: 4.712A pdb=" N MET F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 173 " --> pdb=" O ILE F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.581A pdb=" N LEU F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.355A pdb=" N MET F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 111 through 125 removed outlier: 4.316A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 178 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 269 through 279 Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.507A pdb=" N MET G 289 " --> pdb=" O GLU G 285 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 297 " --> pdb=" O ALA G 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.571A pdb=" N ALA H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP H 58 " --> pdb=" O ASN H 55 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS H 59 " --> pdb=" O ASP H 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 59' Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.914A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY H 126 " --> pdb=" O ASN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 225 through 234 removed outlier: 3.666A pdb=" N ILE H 229 " --> pdb=" O HIS H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 279 removed outlier: 4.448A pdb=" N ASP H 275 " --> pdb=" O PHE H 271 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 removed outlier: 4.135A pdb=" N GLN H 288 " --> pdb=" O THR H 284 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET H 289 " --> pdb=" O GLU H 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU H 295 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG H 297 " --> pdb=" O ALA H 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 49 Processing helix chain 'I' and resid 50 through 53 removed outlier: 3.720A pdb=" N GLY I 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 83 through 91 WARNING: missing atoms! removed outlier: 3.742A pdb=" N LEU I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 131 Processing helix chain 'I' and resid 134 through 142 removed outlier: 3.910A pdb=" N ALA I 138 " --> pdb=" O SER I 134 " (cutoff:3.500A) 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 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 140 removed outlier: 3.614A pdb=" N PHE A 140 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 165 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 24 " --> pdb=" O PHE A 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 50 through 59 removed outlier: 7.695A pdb=" N VAL B 50 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU B 103 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 52 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS B 101 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 54 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 99 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 59 removed outlier: 7.695A pdb=" N VAL B 50 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU B 103 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 52 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N CYS B 101 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SER B 54 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 99 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 163 removed outlier: 7.210A pdb=" N LEU B 207 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS B 188 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR B 209 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR B 186 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 211 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 215 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 180 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.545A pdb=" N LYS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 46 Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AB6, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.556A pdb=" N GLU D 204 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 214 " --> pdb=" O GLU D 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.710A pdb=" N GLY E 299 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing sheet with id=AB8, 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 25 current: chain 'E' and resid 140 through 144 Processing sheet with id=AB9, first strand: chain 'E' and resid 35 through 36 removed outlier: 3.692A pdb=" N THR E 35 " --> pdb=" O ALA E 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 42 through 46 Processing sheet with id=AC2, first strand: chain 'E' and resid 203 through 204 removed outlier: 4.323A pdb=" N GLN E 214 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 235 through 237 removed outlier: 3.549A pdb=" N ILE E 247 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 254 through 255 removed outlier: 3.618A 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: 4.496A 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 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 25 current: chain 'F' and resid 141 through 144 Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 3.627A pdb=" N THR F 35 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 42 through 47 removed outlier: 8.344A pdb=" N SER F 212 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR F 64 " --> pdb=" O SER F 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'G' and resid 16 through 18 Processing sheet with id=AD2, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.505A pdb=" N LYS G 186 " --> pdb=" O THR G 144 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL G 142 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 42 through 47 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AD5, 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 139 through 145 Processing sheet with id=AD6, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AD7, first strand: chain 'H' and resid 42 through 45 Processing sheet with id=AD8, first strand: chain 'I' and resid 59 through 61 Processing sheet with id=AD9, first strand: chain 'I' and resid 112 through 113 Processing sheet with id=AE1, first strand: chain 'I' and resid 155 through 159 560 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5651 1.33 - 1.45: 3255 1.45 - 1.57: 10159 1.57 - 1.69: 97 1.69 - 1.81: 123 Bond restraints: 19285 Sorted by residual: bond pdb=" CA VAL G 206 " pdb=" CB VAL G 206 " ideal model delta sigma weight residual 1.542 1.560 -0.018 1.55e-02 4.16e+03 1.34e+00 bond pdb=" CB ASP F 226 " pdb=" CG ASP F 226 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.62e-02 3.81e+03 9.94e-01 bond pdb=" CA MET A 1 " pdb=" C MET A 1 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.10e-02 2.27e+03 8.88e-01 bond pdb=" CG LEU D 270 " pdb=" CD1 LEU D 270 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.87e-01 ... (remaining 19280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 25667 1.71 - 3.43: 552 3.43 - 5.14: 62 5.14 - 6.86: 13 6.86 - 8.57: 4 Bond angle restraints: 26298 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 125.66 132.04 -6.38 1.85e+00 2.92e-01 1.19e+01 angle pdb=" N ILE A 75 " pdb=" CA ILE A 75 " pdb=" C ILE A 75 " ideal model delta sigma weight residual 113.16 108.09 5.07 1.49e+00 4.50e-01 1.16e+01 angle pdb=" C LEU E 107 " pdb=" N GLU E 108 " pdb=" CA GLU E 108 " ideal model delta sigma weight residual 125.66 131.41 -5.75 1.85e+00 2.92e-01 9.66e+00 angle pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " pdb=" CG GLU C 108 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.57e+00 angle pdb=" C ASN E 73 " pdb=" N LYS E 74 " pdb=" CA LYS E 74 " ideal model delta sigma weight residual 121.87 128.15 -6.28 2.24e+00 1.99e-01 7.87e+00 ... (remaining 26293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 10630 26.79 - 53.57: 513 53.57 - 80.36: 97 80.36 - 107.14: 11 107.14 - 133.93: 1 Dihedral angle restraints: 11252 sinusoidal: 4707 harmonic: 6545 Sorted by residual: dihedral pdb=" O4' U M 27 " pdb=" C1' U M 27 " pdb=" N1 U M 27 " pdb=" C2 U M 27 " ideal model delta sinusoidal sigma weight residual 200.00 66.07 133.93 1 1.50e+01 4.44e-03 7.23e+01 dihedral pdb=" CA ARG G 131 " pdb=" C ARG G 131 " pdb=" N ASN G 132 " pdb=" CA ASN G 132 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA TRP G 130 " pdb=" C TRP G 130 " pdb=" N ARG G 131 " pdb=" CA ARG G 131 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 11249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2431 0.054 - 0.108: 429 0.108 - 0.162: 70 0.162 - 0.216: 3 0.216 - 0.270: 1 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CB ILE A 2 " pdb=" CA ILE A 2 " pdb=" CG1 ILE A 2 " pdb=" CG2 ILE A 2 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB THR H 268 " pdb=" CA THR H 268 " pdb=" OG1 THR H 268 " pdb=" CG2 THR H 268 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR G 235 " pdb=" CA THR G 235 " pdb=" OG1 THR G 235 " pdb=" CG2 THR G 235 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2931 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 6 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO G 7 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 116 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 117 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 226 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C ASP F 226 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP F 226 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 227 " 0.009 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 749 2.71 - 3.26: 18518 3.26 - 3.80: 27265 3.80 - 4.35: 34396 4.35 - 4.90: 58053 Nonbonded interactions: 138981 Sorted by model distance: nonbonded pdb=" OH TYR G 117 " pdb=" O ASP G 161 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 13 " pdb=" OE1 GLU D 93 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN B 184 " pdb=" OG1 THR B 211 " model vdw 2.193 3.040 nonbonded pdb=" O TRP D 130 " pdb=" N ASN D 132 " model vdw 2.214 3.120 nonbonded pdb=" N MET A 1 " pdb=" OE2 GLU A 4 " model vdw 2.220 3.120 ... (remaining 138976 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' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'E' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'F' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'G' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'H' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) } 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=0.06 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.380 Find NCS groups from input model: 0.650 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.003 0.034 19285 Z= 0.134 Angle : 0.604 8.573 26298 Z= 0.336 Chirality : 0.042 0.270 2934 Planarity : 0.004 0.055 3316 Dihedral : 15.511 133.927 7178 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.71 (0.17), residues: 2380 helix: 0.47 (0.23), residues: 526 sheet: -0.17 (0.25), residues: 474 loop : -2.25 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 PHE 0.015 0.001 PHE H 150 TYR 0.026 0.001 TYR D 240 ARG 0.006 0.000 ARG H 257 Details of bonding type rmsd hydrogen bonds : bond 0.12921 ( 534) hydrogen bonds : angle 5.77219 ( 1545) covalent geometry : bond 0.00276 (19285) covalent geometry : angle 0.60366 (26298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5183 (OUTLIER) cc_final: 0.4865 (p0) REVERT: A 142 GLN cc_start: 0.7915 (pp30) cc_final: 0.7506 (pp30) REVERT: A 150 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 198 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8043 (ttm) REVERT: F 88 ASP cc_start: 0.7984 (t70) cc_final: 0.7578 (t70) outliers start: 2 outliers final: 1 residues processed: 308 average time/residue: 0.3153 time to fit residues: 151.4930 Evaluate side-chains 250 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain G residue 19 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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** C 203 GLN D 158 ASN G 48 GLN G 63 GLN H 66 ASN H 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.146720 restraints weight = 32093.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144396 restraints weight = 24398.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145784 restraints weight = 22961.572| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19285 Z= 0.143 Angle : 0.589 10.098 26298 Z= 0.315 Chirality : 0.043 0.196 2934 Planarity : 0.004 0.046 3316 Dihedral : 13.227 132.933 3293 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 1.31 % Allowed : 8.92 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.67 (0.17), residues: 2380 helix: 0.47 (0.23), residues: 537 sheet: -0.22 (0.25), residues: 477 loop : -2.21 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 130 HIS 0.002 0.001 HIS F 72 PHE 0.032 0.001 PHE B 226 TYR 0.025 0.001 TYR D 240 ARG 0.002 0.000 ARG C 133 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 534) hydrogen bonds : angle 4.84298 ( 1545) covalent geometry : bond 0.00322 (19285) covalent geometry : angle 0.58853 (26298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.3823 (t80) REVERT: A 128 THR cc_start: 0.6348 (p) cc_final: 0.6124 (p) REVERT: A 142 GLN cc_start: 0.7823 (pp30) cc_final: 0.7329 (pp30) REVERT: A 150 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7946 (tm-30) REVERT: A 165 GLN cc_start: 0.4994 (mp10) cc_final: 0.4584 (mp10) REVERT: C 103 LEU cc_start: 0.8988 (tp) cc_final: 0.8741 (tp) REVERT: C 285 GLU cc_start: 0.8117 (pp20) cc_final: 0.7779 (pp20) REVERT: E 289 MET cc_start: 0.8228 (ttm) cc_final: 0.7954 (ttm) REVERT: F 88 ASP cc_start: 0.7990 (t70) cc_final: 0.7723 (t70) REVERT: F 226 ASP cc_start: 0.7910 (p0) cc_final: 0.7692 (p0) REVERT: H 191 MET cc_start: 0.8007 (ttm) cc_final: 0.7716 (ttp) outliers start: 24 outliers final: 19 residues processed: 286 average time/residue: 0.2848 time to fit residues: 128.1560 Evaluate side-chains 266 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.152184 restraints weight = 29156.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150599 restraints weight = 39255.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.152909 restraints weight = 27291.000| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19285 Z= 0.148 Angle : 0.577 8.618 26298 Z= 0.307 Chirality : 0.042 0.177 2934 Planarity : 0.003 0.041 3316 Dihedral : 13.172 130.669 3290 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 1.63 % Allowed : 12.73 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.62 (0.17), residues: 2380 helix: 0.64 (0.23), residues: 528 sheet: -0.32 (0.24), residues: 489 loop : -2.18 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 231 HIS 0.003 0.001 HIS E 189 PHE 0.015 0.001 PHE B 226 TYR 0.025 0.002 TYR D 240 ARG 0.003 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 534) hydrogen bonds : angle 4.68198 ( 1545) covalent geometry : bond 0.00336 (19285) covalent geometry : angle 0.57673 (26298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.6481 (t80) cc_final: 0.5570 (t80) REVERT: A 112 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.3397 (t80) REVERT: A 142 GLN cc_start: 0.7880 (pp30) cc_final: 0.7297 (pp30) REVERT: A 150 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 165 GLN cc_start: 0.5256 (mp10) cc_final: 0.4761 (mp10) REVERT: C 103 LEU cc_start: 0.9043 (tp) cc_final: 0.8812 (tp) REVERT: C 158 ASN cc_start: 0.6850 (t0) cc_final: 0.6537 (t0) REVERT: D 289 MET cc_start: 0.7578 (mtm) cc_final: 0.7342 (mtm) REVERT: D 292 THR cc_start: 0.9160 (t) cc_final: 0.8947 (t) REVERT: E 289 MET cc_start: 0.8102 (ttm) cc_final: 0.7718 (ttm) REVERT: F 88 ASP cc_start: 0.8010 (t70) cc_final: 0.7725 (t70) REVERT: H 14 ARG cc_start: 0.3422 (mpt90) cc_final: 0.2954 (mmt180) outliers start: 30 outliers final: 25 residues processed: 284 average time/residue: 0.3237 time to fit residues: 147.9515 Evaluate side-chains 284 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 43 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 ASN ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.186312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143809 restraints weight = 27035.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143034 restraints weight = 27405.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141975 restraints weight = 29709.015| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 19285 Z= 0.319 Angle : 0.738 8.276 26298 Z= 0.394 Chirality : 0.047 0.202 2934 Planarity : 0.005 0.060 3316 Dihedral : 13.637 130.043 3290 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.95 % Favored : 86.96 % Rotamer: Outliers : 2.99 % Allowed : 15.67 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.20 (0.17), residues: 2380 helix: 0.28 (0.23), residues: 523 sheet: -1.12 (0.23), residues: 516 loop : -2.41 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 130 HIS 0.007 0.002 HIS F 225 PHE 0.030 0.003 PHE G 200 TYR 0.037 0.002 TYR D 240 ARG 0.008 0.001 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 534) hydrogen bonds : angle 5.21946 ( 1545) covalent geometry : bond 0.00744 (19285) covalent geometry : angle 0.73760 (26298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5459 (mp) cc_final: 0.4204 (tp) REVERT: A 112 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.3589 (t80) REVERT: A 142 GLN cc_start: 0.7624 (pp30) cc_final: 0.6829 (pp30) REVERT: A 165 GLN cc_start: 0.4897 (mp10) cc_final: 0.4529 (mp10) REVERT: C 158 ASN cc_start: 0.7111 (t0) cc_final: 0.6808 (t0) REVERT: C 250 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6367 (mm-30) REVERT: F 88 ASP cc_start: 0.8077 (t70) cc_final: 0.7546 (t70) REVERT: F 205 PHE cc_start: 0.8263 (t80) cc_final: 0.8034 (t80) REVERT: G 139 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7837 (pt) REVERT: G 182 PHE cc_start: 0.8164 (p90) cc_final: 0.7961 (p90) REVERT: G 244 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7631 (p) outliers start: 55 outliers final: 40 residues processed: 294 average time/residue: 0.2902 time to fit residues: 132.2175 Evaluate side-chains 272 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 188 optimal weight: 4.9990 chunk 196 optimal weight: 0.0870 chunk 147 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 48 GLN F 227 GLN G 279 ASN H 72 HIS H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147641 restraints weight = 32866.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146572 restraints weight = 26953.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148028 restraints weight = 24820.221| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19285 Z= 0.116 Angle : 0.582 8.592 26298 Z= 0.310 Chirality : 0.042 0.166 2934 Planarity : 0.004 0.043 3316 Dihedral : 13.127 127.112 3290 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.29 % Allowed : 17.85 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.72 (0.17), residues: 2380 helix: 0.61 (0.23), residues: 528 sheet: -0.49 (0.24), residues: 507 loop : -2.24 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 130 HIS 0.013 0.001 HIS H 72 PHE 0.017 0.001 PHE B 202 TYR 0.019 0.001 TYR B 52 ARG 0.012 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 534) hydrogen bonds : angle 4.61584 ( 1545) covalent geometry : bond 0.00252 (19285) covalent geometry : angle 0.58234 (26298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4665 (mp) cc_final: 0.3541 (mt) REVERT: A 112 TYR cc_start: 0.4758 (OUTLIER) cc_final: 0.3309 (t80) REVERT: A 142 GLN cc_start: 0.7709 (pp30) cc_final: 0.7036 (pp30) REVERT: A 150 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 165 GLN cc_start: 0.5096 (mp10) cc_final: 0.4601 (mp10) REVERT: B 26 MET cc_start: 0.7722 (mmm) cc_final: 0.7260 (mmm) REVERT: C 158 ASN cc_start: 0.6879 (t0) cc_final: 0.6589 (t0) REVERT: C 250 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5992 (mm-30) REVERT: D 107 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8000 (mm) REVERT: D 292 THR cc_start: 0.9228 (t) cc_final: 0.9023 (t) REVERT: D 294 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7886 (t0) REVERT: E 289 MET cc_start: 0.8451 (ttm) cc_final: 0.8212 (ttm) REVERT: F 88 ASP cc_start: 0.8046 (t70) cc_final: 0.7510 (t70) REVERT: G 139 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7945 (pt) REVERT: G 235 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7647 (t) REVERT: H 192 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7360 (tt) outliers start: 42 outliers final: 25 residues processed: 296 average time/residue: 0.2760 time to fit residues: 126.9766 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 139 optimal weight: 0.9980 chunk 47 optimal weight: 0.0170 chunk 149 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 166 optimal weight: 0.0040 chunk 156 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 294 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.194155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141144 restraints weight = 39234.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141959 restraints weight = 20904.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142796 restraints weight = 15769.600| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19285 Z= 0.104 Angle : 0.566 9.310 26298 Z= 0.297 Chirality : 0.041 0.165 2934 Planarity : 0.003 0.042 3316 Dihedral : 12.999 126.330 3290 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.45 % Allowed : 18.93 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.55 (0.17), residues: 2380 helix: 0.83 (0.24), residues: 528 sheet: -0.39 (0.24), residues: 501 loop : -2.16 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 PHE 0.016 0.001 PHE B 202 TYR 0.017 0.001 TYR B 52 ARG 0.010 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 534) hydrogen bonds : angle 4.44475 ( 1545) covalent geometry : bond 0.00225 (19285) covalent geometry : angle 0.56567 (26298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5610 (mp) cc_final: 0.4655 (mt) REVERT: A 106 PHE cc_start: 0.7561 (t80) cc_final: 0.7346 (t80) REVERT: A 112 TYR cc_start: 0.4822 (OUTLIER) cc_final: 0.3583 (t80) REVERT: A 142 GLN cc_start: 0.7601 (pp30) cc_final: 0.6880 (pp30) REVERT: A 150 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 165 GLN cc_start: 0.4517 (mp10) cc_final: 0.4114 (mp10) REVERT: B 177 ARG cc_start: 0.9282 (mmm160) cc_final: 0.9023 (mmp80) REVERT: C 158 ASN cc_start: 0.7075 (t0) cc_final: 0.6733 (t0) REVERT: C 250 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6174 (mm-30) REVERT: D 292 THR cc_start: 0.9208 (t) cc_final: 0.9006 (t) REVERT: D 294 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7882 (t0) REVERT: E 289 MET cc_start: 0.8486 (ttm) cc_final: 0.8216 (ttm) REVERT: F 88 ASP cc_start: 0.8042 (t70) cc_final: 0.7494 (t70) REVERT: G 235 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7568 (t) REVERT: H 192 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7339 (tt) outliers start: 45 outliers final: 25 residues processed: 297 average time/residue: 0.2739 time to fit residues: 128.1131 Evaluate side-chains 282 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 200 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.190354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136105 restraints weight = 38721.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137144 restraints weight = 21668.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137551 restraints weight = 17248.885| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19285 Z= 0.174 Angle : 0.621 9.560 26298 Z= 0.328 Chirality : 0.043 0.174 2934 Planarity : 0.004 0.044 3316 Dihedral : 13.154 127.850 3290 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 2.29 % Allowed : 19.70 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.17), residues: 2380 helix: 0.80 (0.23), residues: 523 sheet: -0.56 (0.24), residues: 511 loop : -2.24 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 130 HIS 0.004 0.001 HIS E 72 PHE 0.018 0.002 PHE F 205 TYR 0.023 0.002 TYR D 240 ARG 0.009 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 534) hydrogen bonds : angle 4.61081 ( 1545) covalent geometry : bond 0.00401 (19285) covalent geometry : angle 0.62140 (26298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5664 (mp) cc_final: 0.4788 (tp) REVERT: A 106 PHE cc_start: 0.7653 (t80) cc_final: 0.6756 (t80) REVERT: A 112 TYR cc_start: 0.4764 (OUTLIER) cc_final: 0.3284 (t80) REVERT: A 113 ASP cc_start: 0.7863 (p0) cc_final: 0.7358 (t0) REVERT: A 142 GLN cc_start: 0.7598 (pp30) cc_final: 0.6889 (pp30) REVERT: A 165 GLN cc_start: 0.4553 (mp10) cc_final: 0.4138 (mp10) REVERT: B 26 MET cc_start: 0.8171 (mmm) cc_final: 0.7700 (mmm) REVERT: B 177 ARG cc_start: 0.9341 (mmm160) cc_final: 0.9076 (mmp80) REVERT: C 158 ASN cc_start: 0.7136 (t0) cc_final: 0.6811 (t0) REVERT: C 250 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6319 (mm-30) REVERT: D 107 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8072 (mm) REVERT: E 289 MET cc_start: 0.8578 (ttm) cc_final: 0.8293 (ttm) REVERT: F 88 ASP cc_start: 0.8112 (t70) cc_final: 0.7548 (t70) REVERT: H 192 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7312 (tt) outliers start: 42 outliers final: 29 residues processed: 286 average time/residue: 0.2807 time to fit residues: 125.6089 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 241 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 136 optimal weight: 0.0050 chunk 194 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN F 227 GLN G 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.194193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139118 restraints weight = 38892.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141434 restraints weight = 22106.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142365 restraints weight = 14846.741| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19285 Z= 0.109 Angle : 0.583 11.058 26298 Z= 0.304 Chirality : 0.041 0.186 2934 Planarity : 0.003 0.041 3316 Dihedral : 12.913 126.407 3290 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.01 % Allowed : 20.24 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.46 (0.17), residues: 2380 helix: 0.95 (0.24), residues: 528 sheet: -0.32 (0.24), residues: 501 loop : -2.13 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 PHE 0.016 0.001 PHE B 202 TYR 0.017 0.001 TYR B 52 ARG 0.007 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02793 ( 534) hydrogen bonds : angle 4.39204 ( 1545) covalent geometry : bond 0.00237 (19285) covalent geometry : angle 0.58350 (26298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 259 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5478 (mp) cc_final: 0.4534 (tp) REVERT: A 106 PHE cc_start: 0.7344 (t80) cc_final: 0.7099 (t80) REVERT: A 112 TYR cc_start: 0.4730 (OUTLIER) cc_final: 0.3470 (t80) REVERT: A 142 GLN cc_start: 0.7658 (pp30) cc_final: 0.6909 (pp30) REVERT: A 165 GLN cc_start: 0.4555 (mp10) cc_final: 0.4114 (mp10) REVERT: B 155 MET cc_start: 0.8082 (ppp) cc_final: 0.7869 (ppp) REVERT: C 158 ASN cc_start: 0.7014 (t0) cc_final: 0.6658 (t0) REVERT: C 250 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6492 (mm-30) REVERT: D 292 THR cc_start: 0.9242 (t) cc_final: 0.9034 (t) REVERT: E 289 MET cc_start: 0.8426 (ttm) cc_final: 0.8221 (ttm) REVERT: F 88 ASP cc_start: 0.7999 (t70) cc_final: 0.7410 (t70) REVERT: G 250 GLU cc_start: 0.7846 (mp0) cc_final: 0.7541 (mm-30) REVERT: H 192 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7256 (tt) outliers start: 37 outliers final: 29 residues processed: 285 average time/residue: 0.2894 time to fit residues: 130.1025 Evaluate side-chains 284 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 166 optimal weight: 0.4980 chunk 144 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 0.0010 chunk 185 optimal weight: 0.3980 chunk 147 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 224 optimal weight: 30.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN D 294 ASN F 227 GLN G 48 GLN G 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.192901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150974 restraints weight = 30000.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150318 restraints weight = 36606.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151638 restraints weight = 27700.589| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19285 Z= 0.125 Angle : 0.595 12.459 26298 Z= 0.308 Chirality : 0.042 0.166 2934 Planarity : 0.003 0.042 3316 Dihedral : 12.929 126.930 3290 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.96 % Allowed : 20.89 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.45 (0.17), residues: 2380 helix: 0.94 (0.24), residues: 528 sheet: -0.30 (0.24), residues: 501 loop : -2.13 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 72 PHE 0.017 0.001 PHE F 205 TYR 0.018 0.001 TYR D 240 ARG 0.007 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02935 ( 534) hydrogen bonds : angle 4.36051 ( 1545) covalent geometry : bond 0.00283 (19285) covalent geometry : angle 0.59505 (26298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4790 (mp) cc_final: 0.3839 (tp) REVERT: A 112 TYR cc_start: 0.4708 (OUTLIER) cc_final: 0.3415 (t80) REVERT: A 142 GLN cc_start: 0.7732 (pp30) cc_final: 0.7042 (pp30) REVERT: A 165 GLN cc_start: 0.4905 (mp10) cc_final: 0.4384 (mp10) REVERT: C 158 ASN cc_start: 0.7010 (t0) cc_final: 0.6674 (t0) REVERT: D 292 THR cc_start: 0.9233 (t) cc_final: 0.9029 (t) REVERT: F 88 ASP cc_start: 0.8012 (t70) cc_final: 0.7489 (t70) REVERT: F 165 ASP cc_start: 0.7683 (t70) cc_final: 0.7168 (t0) REVERT: G 182 PHE cc_start: 0.7908 (p90) cc_final: 0.7618 (p90) REVERT: G 250 GLU cc_start: 0.7690 (mp0) cc_final: 0.7431 (mm-30) REVERT: H 192 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7370 (tt) outliers start: 36 outliers final: 33 residues processed: 277 average time/residue: 0.2704 time to fit residues: 118.7295 Evaluate side-chains 285 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 229 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN C 101 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 GLN G 279 ASN H 225 HIS H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.183457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127056 restraints weight = 37040.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129634 restraints weight = 22625.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.132384 restraints weight = 15648.936| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 19285 Z= 0.416 Angle : 0.867 15.746 26298 Z= 0.456 Chirality : 0.052 0.219 2934 Planarity : 0.006 0.059 3316 Dihedral : 13.658 129.849 3290 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.88 % Favored : 86.04 % Rotamer: Outliers : 2.45 % Allowed : 20.57 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.32 (0.17), residues: 2380 helix: 0.10 (0.23), residues: 529 sheet: -0.85 (0.24), residues: 469 loop : -2.60 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 130 HIS 0.010 0.002 HIS F 225 PHE 0.039 0.003 PHE G 200 TYR 0.040 0.003 TYR C 99 ARG 0.008 0.001 ARG C 234 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 534) hydrogen bonds : angle 5.27277 ( 1545) covalent geometry : bond 0.00972 (19285) covalent geometry : angle 0.86734 (26298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5825 (mp) cc_final: 0.4871 (tp) REVERT: A 112 TYR cc_start: 0.4540 (OUTLIER) cc_final: 0.2975 (t80) REVERT: A 113 ASP cc_start: 0.8069 (p0) cc_final: 0.7491 (t0) REVERT: A 142 GLN cc_start: 0.7636 (pp30) cc_final: 0.6836 (pp30) REVERT: A 165 GLN cc_start: 0.4691 (mp10) cc_final: 0.4231 (mp10) REVERT: B 173 ASP cc_start: 0.5579 (t0) cc_final: 0.5343 (t0) REVERT: B 182 MET cc_start: 0.8583 (tpp) cc_final: 0.7842 (tmm) REVERT: C 158 ASN cc_start: 0.7152 (t0) cc_final: 0.6876 (t0) REVERT: E 72 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.7511 (t70) REVERT: E 104 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (mm110) REVERT: F 88 ASP cc_start: 0.8070 (t70) cc_final: 0.7519 (t70) REVERT: G 129 LEU cc_start: 0.8328 (tt) cc_final: 0.7915 (tp) REVERT: G 139 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8130 (pt) REVERT: G 267 LYS cc_start: 0.8140 (tppt) cc_final: 0.7914 (ttpt) REVERT: H 192 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7336 (tt) outliers start: 45 outliers final: 31 residues processed: 279 average time/residue: 0.2763 time to fit residues: 120.0993 Evaluate side-chains 270 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 288 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 198 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.184071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141399 restraints weight = 27178.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140038 restraints weight = 36263.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141436 restraints weight = 28548.084| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.209 19285 Z= 0.356 Angle : 0.973 59.177 26298 Z= 0.535 Chirality : 0.055 1.439 2934 Planarity : 0.005 0.059 3316 Dihedral : 13.660 129.858 3290 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.84 % Favored : 86.08 % Rotamer: Outliers : 2.23 % Allowed : 20.95 % Favored : 76.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.37 (0.16), residues: 2380 helix: 0.02 (0.22), residues: 534 sheet: -0.90 (0.24), residues: 469 loop : -2.60 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 130 HIS 0.008 0.002 HIS F 225 PHE 0.035 0.003 PHE G 200 TYR 0.034 0.003 TYR C 99 ARG 0.008 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 534) hydrogen bonds : angle 5.26253 ( 1545) covalent geometry : bond 0.00830 (19285) covalent geometry : angle 0.97332 (26298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.36 seconds wall clock time: 114 minutes 9.91 seconds (6849.91 seconds total)