Starting phenix.real_space_refine on Sun Sep 13 08:44:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2026/7wwu_32873.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'HIS:plan': 1, 'ASP: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: {'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 8, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 1} 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: {'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 8, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 1} 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, 'RNAv2': 49} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 10, 'rna3p_pyr': 20} Link IDs: {'rna2p': 18, 'rna3p': 31} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.11, per 1000 atoms: 0.27 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: 1.57 Conformation dependent library (CDL) restraints added in 953.6 milliseconds 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: 1.96 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: 2.95 Time building geometry restraints manager: 2.12 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: 25463 1.71 - 3.43: 698 3.43 - 5.14: 116 5.14 - 6.86: 14 6.86 - 8.57: 4 Bond angle restraints: 26295 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=" O3' G M 9 " pdb=" C3' G M 9 " pdb=" C2' G M 9 " ideal model delta sigma weight residual 113.80 108.17 5.63 2.00e+00 2.50e-01 7.94e+00 ... (remaining 26290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 9753 17.28 - 34.56: 1012 34.56 - 51.84: 200 51.84 - 69.13: 90 69.13 - 86.41: 34 Dihedral angle restraints: 11089 sinusoidal: 4544 harmonic: 6545 Sorted by residual: dihedral pdb=" C4' G M 9 " pdb=" C3' G M 9 " pdb=" C2' G M 9 " pdb=" C1' G M 9 " ideal model delta sinusoidal sigma weight residual 36.35 -38.32 74.66 1 3.10e+00 1.04e-01 7.35e+02 dihedral pdb=" C4' G M 20 " pdb=" C3' G M 20 " pdb=" C2' G M 20 " pdb=" C1' G M 20 " ideal model delta sinusoidal sigma weight residual 36.34 -36.82 73.16 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' A M 37 " pdb=" C3' A M 37 " pdb=" C2' A M 37 " pdb=" C1' A M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -36.37 72.71 1 3.10e+00 1.04e-01 7.02e+02 ... (remaining 11086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2425 0.059 - 0.118: 386 0.118 - 0.176: 36 0.176 - 0.235: 37 0.235 - 0.294: 50 Chirality restraints: 2934 Sorted by residual: chirality pdb=" C3' G M 9 " pdb=" C4' G M 9 " pdb=" O3' G M 9 " pdb=" C2' G M 9 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' U M 35 " pdb=" C3' U M 35 " pdb=" O2' U M 35 " pdb=" C1' U M 35 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' U M 22 " pdb=" C3' U M 22 " pdb=" O2' U M 22 " pdb=" C1' U M 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.960 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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= 0.138 Angle : 0.668 8.573 26295 Z= 0.353 Chirality : 0.059 0.294 2934 Planarity : 0.004 0.055 3316 Dihedral : 15.615 86.408 7015 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (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 ARG 0.006 0.000 ARG H 257 TYR 0.026 0.001 TYR D 240 PHE 0.015 0.001 PHE H 150 TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (19285) covalent geometry : angle 0.66850 / 0.35 (26295) hydrogen bonds : bond 0.12921 / 8.58 ( 534) hydrogen bonds : angle 5.77219 / 4.09 ( 1545) *********************** 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 : 0.687 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: 0.8498 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8044 (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: 0.1279 time to fit residues: 62.5717 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 : 0.617 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN D 158 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN G 63 GLN H 66 ASN 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 = 0.4253 r_free = 0.4253 target = 0.192032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144395 restraints weight = 31615.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141960 restraints weight = 22346.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143075 restraints weight = 23047.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143750 restraints weight = 15800.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144360 restraints weight = 13846.215| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19285 Z= 0.222 Angle : 0.870 17.343 26295 Z= 0.402 Chirality : 0.074 1.025 2934 Planarity : 0.004 0.048 3316 Dihedral : 11.865 155.283 3130 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.77 % Favored : 89.19 % Rotamer: Outliers : 1.58 % Allowed : 9.30 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2380 helix: 0.39 (0.23), residues: 531 sheet: -0.57 (0.24), residues: 497 loop : -2.30 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 131 TYR 0.030 0.002 TYR D 240 PHE 0.033 0.002 PHE B 226 TRP 0.021 0.002 TRP D 130 HIS 0.003 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (19285) covalent geometry : angle 0.86978 / 0.40 (26295) hydrogen bonds : bond 0.04030 / 2.57 ( 534) hydrogen bonds : angle 5.06374 / 3.54 ( 1545) *********************** 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 290 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.3719 (t80) REVERT: A 142 GLN cc_start: 0.7932 (pp30) cc_final: 0.7357 (pp30) REVERT: A 150 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 165 GLN cc_start: 0.5006 (mp10) cc_final: 0.4570 (mp10) REVERT: C 103 LEU cc_start: 0.9018 (tp) cc_final: 0.8785 (tp) REVERT: C 130 TRP cc_start: 0.6978 (m100) cc_final: 0.6705 (m100) REVERT: C 158 ASN cc_start: 0.7230 (t0) cc_final: 0.6925 (t0) REVERT: E 289 MET cc_start: 0.8119 (ttm) cc_final: 0.7910 (ttm) REVERT: F 88 ASP cc_start: 0.8043 (t70) cc_final: 0.7544 (t70) REVERT: H 14 ARG cc_start: 0.2805 (mpt90) cc_final: 0.2182 (mmt180) outliers start: 29 outliers final: 24 residues processed: 277 average time/residue: 0.1288 time to fit residues: 56.7491 Evaluate side-chains 262 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR 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 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 193 LEU 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 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 187 VAL 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 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 247 ILE 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 151 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 197 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.195888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139253 restraints weight = 36790.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143144 restraints weight = 21172.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145030 restraints weight = 13403.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145404 restraints weight = 12990.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145650 restraints weight = 11588.106| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19285 Z= 0.127 Angle : 0.673 10.159 26295 Z= 0.326 Chirality : 0.053 0.386 2934 Planarity : 0.003 0.042 3316 Dihedral : 11.883 168.817 3127 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2380 helix: 0.66 (0.23), residues: 523 sheet: -0.43 (0.24), residues: 501 loop : -2.19 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 257 TYR 0.021 0.001 TYR D 240 PHE 0.016 0.001 PHE F 205 TRP 0.027 0.002 TRP B 231 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (19285) covalent geometry : angle 0.67254 / 0.33 (26295) hydrogen bonds : bond 0.03109 / 1.99 ( 534) hydrogen bonds : angle 4.61645 / 3.23 ( 1545) *********************** 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 295 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5647 (mp) cc_final: 0.4479 (mt) REVERT: A 106 PHE cc_start: 0.7384 (t80) cc_final: 0.6503 (t80) REVERT: A 107 LYS cc_start: 0.7767 (tppt) cc_final: 0.7510 (tppt) REVERT: A 112 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.3506 (t80) REVERT: A 113 ASP cc_start: 0.8487 (p0) cc_final: 0.8277 (t0) REVERT: A 142 GLN cc_start: 0.7789 (pp30) cc_final: 0.7170 (pp30) REVERT: A 150 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 165 GLN cc_start: 0.4726 (mp10) cc_final: 0.4306 (mp10) REVERT: B 63 ARG cc_start: 0.8057 (mmp-170) cc_final: 0.7824 (mmp-170) REVERT: B 182 MET cc_start: 0.7623 (tpp) cc_final: 0.7083 (tmm) REVERT: B 235 GLU cc_start: 0.8756 (tp30) cc_final: 0.8549 (tp30) REVERT: C 103 LEU cc_start: 0.8917 (tp) cc_final: 0.8672 (tp) REVERT: C 158 ASN cc_start: 0.6775 (t0) cc_final: 0.6446 (t0) REVERT: D 191 MET cc_start: 0.7732 (mtm) cc_final: 0.7394 (mtt) REVERT: D 292 THR cc_start: 0.9166 (t) cc_final: 0.8936 (t) REVERT: F 88 ASP cc_start: 0.8001 (t70) cc_final: 0.7692 (t70) REVERT: H 14 ARG cc_start: 0.2747 (mpt90) cc_final: 0.1611 (mmt180) outliers start: 30 outliers final: 22 residues processed: 284 average time/residue: 0.1237 time to fit residues: 56.1370 Evaluate side-chains 271 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR 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 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 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 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 25 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 223 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 227 optimal weight: 40.0000 chunk 138 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 203 GLN C 231 ASN F 227 GLN 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 = 0.4265 r_free = 0.4265 target = 0.193157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152698 restraints weight = 29389.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152406 restraints weight = 38427.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153585 restraints weight = 27817.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154908 restraints weight = 16184.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158006 restraints weight = 13520.738| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19285 Z= 0.168 Angle : 0.685 9.531 26295 Z= 0.334 Chirality : 0.054 0.398 2934 Planarity : 0.004 0.043 3316 Dihedral : 11.921 169.776 3127 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2380 helix: 0.70 (0.23), residues: 523 sheet: -0.46 (0.24), residues: 499 loop : -2.23 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 234 TYR 0.024 0.002 TYR D 240 PHE 0.016 0.001 PHE D 67 TRP 0.019 0.002 TRP D 130 HIS 0.003 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (19285) covalent geometry : angle 0.68545 / 0.33 (26295) hydrogen bonds : bond 0.03399 / 2.16 ( 534) hydrogen bonds : angle 4.62199 / 3.24 ( 1545) *********************** 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 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5667 (p0) cc_final: 0.5457 (p0) REVERT: A 66 LEU cc_start: 0.4775 (mp) cc_final: 0.3456 (mt) REVERT: A 112 TYR cc_start: 0.4833 (OUTLIER) cc_final: 0.3537 (t80) REVERT: A 142 GLN cc_start: 0.7838 (pp30) cc_final: 0.7191 (pp30) REVERT: A 150 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 165 GLN cc_start: 0.5195 (mp10) cc_final: 0.4697 (mp10) REVERT: B 26 MET cc_start: 0.7406 (mmm) cc_final: 0.6901 (mmm) REVERT: C 103 LEU cc_start: 0.9054 (tp) cc_final: 0.8818 (tp) REVERT: C 130 TRP cc_start: 0.7083 (m100) cc_final: 0.6820 (m100) REVERT: C 158 ASN cc_start: 0.6756 (t0) cc_final: 0.6483 (t0) REVERT: C 250 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6009 (mm-30) REVERT: F 88 ASP cc_start: 0.7929 (t70) cc_final: 0.7626 (t70) REVERT: G 139 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7840 (pt) REVERT: H 14 ARG cc_start: 0.3638 (mpt90) cc_final: 0.3029 (mmt180) outliers start: 41 outliers final: 27 residues processed: 289 average time/residue: 0.1289 time to fit residues: 59.7528 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 268 THR 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 104 GLN Chi-restraints excluded: chain E residue 156 LEU 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 139 ILE Chi-restraints excluded: chain G residue 140 GLU 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 258 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 211 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 231 ASN E 294 ASN F 227 GLN G 279 ASN 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 = 0.4275 r_free = 0.4275 target = 0.194067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137662 restraints weight = 36647.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140830 restraints weight = 21959.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143147 restraints weight = 14529.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142921 restraints weight = 13545.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143427 restraints weight = 12231.351| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19285 Z= 0.140 Angle : 0.668 10.816 26295 Z= 0.326 Chirality : 0.052 0.328 2934 Planarity : 0.004 0.052 3316 Dihedral : 11.897 170.742 3127 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 2.72 % Allowed : 16.32 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2380 helix: 0.81 (0.23), residues: 523 sheet: -0.42 (0.24), residues: 499 loop : -2.19 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 177 TYR 0.021 0.001 TYR D 240 PHE 0.022 0.001 PHE F 205 TRP 0.021 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19285) covalent geometry : angle 0.66798 / 0.33 (26295) hydrogen bonds : bond 0.03136 / 1.99 ( 534) hydrogen bonds : angle 4.51570 / 3.17 ( 1545) *********************** 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 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 263 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5651 (mp) cc_final: 0.4517 (mt) REVERT: A 112 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.3461 (t80) REVERT: A 142 GLN cc_start: 0.7642 (pp30) cc_final: 0.6956 (pp30) REVERT: A 150 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 165 GLN cc_start: 0.4563 (mp10) cc_final: 0.4153 (mp10) REVERT: C 103 LEU cc_start: 0.8975 (tp) cc_final: 0.8727 (tp) REVERT: C 130 TRP cc_start: 0.7047 (m100) cc_final: 0.6841 (m100) REVERT: C 158 ASN cc_start: 0.6930 (t0) cc_final: 0.6608 (t0) REVERT: C 250 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6049 (mm-30) REVERT: D 191 MET cc_start: 0.7911 (mtm) cc_final: 0.7691 (mtm) REVERT: D 292 THR cc_start: 0.9218 (t) cc_final: 0.9001 (t) REVERT: F 88 ASP cc_start: 0.8037 (t70) cc_final: 0.7689 (t70) REVERT: G 139 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7881 (pt) REVERT: H 14 ARG cc_start: 0.2828 (mpt90) cc_final: 0.2349 (mmt180) REVERT: H 150 PHE cc_start: 0.7405 (m-80) cc_final: 0.7151 (m-80) outliers start: 50 outliers final: 33 residues processed: 299 average time/residue: 0.1270 time to fit residues: 60.9699 Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 231 ASN 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 108 GLU 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 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 48 GLN Chi-restraints excluded: chain G residue 139 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 38 MET Chi-restraints excluded: chain H residue 47 THR 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 258 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 171 optimal weight: 10.0000 chunk 115 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 GLN C 231 ASN F 227 GLN G 279 ASN H 288 GLN ** 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 = 0.4283 r_free = 0.4283 target = 0.194908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153645 restraints weight = 26828.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.151579 restraints weight = 29833.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153013 restraints weight = 28518.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154264 restraints weight = 16661.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155612 restraints weight = 14245.130| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3833 r_free = 0.3833 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19285 Z= 0.123 Angle : 0.650 9.395 26295 Z= 0.317 Chirality : 0.050 0.305 2934 Planarity : 0.003 0.042 3316 Dihedral : 11.846 173.356 3127 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.83 % Allowed : 17.36 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2380 helix: 0.93 (0.24), residues: 523 sheet: -0.37 (0.24), residues: 509 loop : -2.17 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 177 TYR 0.019 0.001 TYR D 240 PHE 0.016 0.001 PHE B 202 TRP 0.020 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19285) covalent geometry : angle 0.64957 / 0.32 (26295) hydrogen bonds : bond 0.02935 / 1.86 ( 534) hydrogen bonds : angle 4.41204 / 3.10 ( 1545) *********************** 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 318 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4715 (mp) cc_final: 0.3668 (tp) REVERT: A 112 TYR cc_start: 0.4577 (OUTLIER) cc_final: 0.3575 (t80) REVERT: A 142 GLN cc_start: 0.7795 (pp30) cc_final: 0.7117 (pp30) REVERT: A 150 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 165 GLN cc_start: 0.5024 (mp10) cc_final: 0.4519 (mp10) REVERT: C 103 LEU cc_start: 0.9051 (tp) cc_final: 0.8796 (tp) REVERT: C 158 ASN cc_start: 0.6961 (t0) cc_final: 0.6670 (t0) REVERT: C 250 GLU cc_start: 0.6245 (mm-30) cc_final: 0.5919 (mm-30) REVERT: D 191 MET cc_start: 0.7893 (mtm) cc_final: 0.7553 (mtt) REVERT: D 292 THR cc_start: 0.9181 (t) cc_final: 0.8975 (t) REVERT: F 88 ASP cc_start: 0.7962 (t70) cc_final: 0.7652 (t70) REVERT: H 14 ARG cc_start: 0.3774 (mpt90) cc_final: 0.3160 (mmt180) outliers start: 52 outliers final: 38 residues processed: 301 average time/residue: 0.1249 time to fit residues: 60.1003 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 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 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 231 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 72 HIS 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 104 GLN Chi-restraints excluded: chain F residue 108 GLU 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 48 GLN Chi-restraints excluded: chain G residue 139 ILE 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 38 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 197 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 226 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN C 231 ASN F 227 GLN H 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 = 0.4250 r_free = 0.4250 target = 0.191627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136425 restraints weight = 36782.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139311 restraints weight = 20859.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139993 restraints weight = 13784.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140983 restraints weight = 13640.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140908 restraints weight = 12444.748| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19285 Z= 0.191 Angle : 0.711 8.926 26295 Z= 0.348 Chirality : 0.054 0.361 2934 Planarity : 0.004 0.063 3316 Dihedral : 11.944 172.000 3127 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.06 % Favored : 88.90 % Rotamer: Outliers : 2.88 % Allowed : 18.17 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.17), residues: 2380 helix: 0.78 (0.23), residues: 523 sheet: -0.47 (0.24), residues: 512 loop : -2.26 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 177 TYR 0.024 0.002 TYR D 240 PHE 0.016 0.002 PHE B 202 TRP 0.016 0.001 TRP D 130 HIS 0.003 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (19285) covalent geometry : angle 0.71130 / 0.35 (26295) hydrogen bonds : bond 0.03474 / 2.20 ( 534) hydrogen bonds : angle 4.58767 / 3.23 ( 1545) *********************** 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 312 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5471 (mp) cc_final: 0.4452 (tp) REVERT: A 112 TYR cc_start: 0.4783 (OUTLIER) cc_final: 0.3422 (t80) REVERT: A 142 GLN cc_start: 0.7718 (pp30) cc_final: 0.6985 (pp30) REVERT: A 150 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 165 GLN cc_start: 0.4728 (mp10) cc_final: 0.4274 (mp10) REVERT: B 173 ASP cc_start: 0.5368 (t0) cc_final: 0.5113 (t0) REVERT: B 182 MET cc_start: 0.7479 (tpp) cc_final: 0.7044 (tmm) REVERT: C 158 ASN cc_start: 0.7088 (t0) cc_final: 0.6784 (t0) REVERT: C 250 GLU cc_start: 0.6483 (mm-30) cc_final: 0.6180 (mm-30) REVERT: F 88 ASP cc_start: 0.8042 (t70) cc_final: 0.7699 (t70) REVERT: G 182 PHE cc_start: 0.8045 (p90) cc_final: 0.7832 (p90) REVERT: H 14 ARG cc_start: 0.2734 (mpt90) cc_final: 0.2336 (mmt180) outliers start: 53 outliers final: 43 residues processed: 298 average time/residue: 0.1298 time to fit residues: 61.4991 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 231 ASN Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 158 ASN 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 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 108 GLU 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 48 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 140 GLU 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 38 MET Chi-restraints excluded: chain H residue 47 THR 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 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 82 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 ASN F 227 GLN ** 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 = 0.4265 r_free = 0.4265 target = 0.193239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152880 restraints weight = 29918.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153451 restraints weight = 37451.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154342 restraints weight = 27558.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155795 restraints weight = 16115.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156709 restraints weight = 13395.990| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19285 Z= 0.142 Angle : 0.682 10.656 26295 Z= 0.334 Chirality : 0.051 0.318 2934 Planarity : 0.003 0.042 3316 Dihedral : 11.905 173.347 3127 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.61 % Allowed : 18.88 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2380 helix: 0.82 (0.23), residues: 523 sheet: -0.42 (0.24), residues: 511 loop : -2.21 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.020 0.001 TYR D 240 PHE 0.016 0.001 PHE B 202 TRP 0.022 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (19285) covalent geometry : angle 0.68233 / 0.33 (26295) hydrogen bonds : bond 0.03122 / 1.98 ( 534) hydrogen bonds : angle 4.50594 / 3.16 ( 1545) *********************** 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 306 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4486 (mp) cc_final: 0.3616 (tp) REVERT: A 112 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.3364 (t80) REVERT: A 142 GLN cc_start: 0.7786 (pp30) cc_final: 0.7122 (pp30) REVERT: A 165 GLN cc_start: 0.5059 (mp10) cc_final: 0.4545 (mp10) REVERT: C 158 ASN cc_start: 0.6991 (t0) cc_final: 0.6710 (t0) REVERT: C 250 GLU cc_start: 0.6272 (mm-30) cc_final: 0.6007 (mm-30) REVERT: D 292 THR cc_start: 0.9236 (t) cc_final: 0.9027 (t) REVERT: F 88 ASP cc_start: 0.7986 (t70) cc_final: 0.7666 (t70) REVERT: G 139 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8134 (pt) REVERT: G 182 PHE cc_start: 0.8034 (p90) cc_final: 0.7833 (p90) REVERT: H 14 ARG cc_start: 0.3337 (mpt90) cc_final: 0.2841 (mmt180) outliers start: 48 outliers final: 41 residues processed: 291 average time/residue: 0.1283 time to fit residues: 59.4161 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 231 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 108 GLU 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 48 GLN Chi-restraints excluded: chain G residue 139 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 38 MET Chi-restraints excluded: chain H residue 47 THR 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 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 127 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 0.0020 chunk 163 optimal weight: 0.7980 chunk 224 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 ASN ** 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 = 0.4245 r_free = 0.4245 target = 0.191328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136744 restraints weight = 36736.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139754 restraints weight = 21043.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139835 restraints weight = 14381.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140903 restraints weight = 14120.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141015 restraints weight = 13391.192| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.004 0.042 19285 Z= 0.183 Angle : 0.720 12.656 26295 Z= 0.351 Chirality : 0.053 0.365 2934 Planarity : 0.004 0.045 3316 Dihedral : 11.959 172.665 3127 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 2.56 % Allowed : 19.15 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2380 helix: 0.64 (0.23), residues: 528 sheet: -0.51 (0.24), residues: 511 loop : -2.25 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.023 0.002 TYR D 240 PHE 0.015 0.002 PHE B 202 TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS F 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (19285) covalent geometry : angle 0.71987 / 0.35 (26295) hydrogen bonds : bond 0.03427 / 2.16 ( 534) hydrogen bonds : angle 4.58548 / 3.22 ( 1545) *********************** 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 303 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 256 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5551 (mp) cc_final: 0.4675 (tp) REVERT: A 112 TYR cc_start: 0.4772 (OUTLIER) cc_final: 0.3556 (t80) REVERT: A 142 GLN cc_start: 0.7684 (pp30) cc_final: 0.6963 (pp30) REVERT: A 165 GLN cc_start: 0.4589 (mp10) cc_final: 0.4156 (mp10) REVERT: B 182 MET cc_start: 0.8268 (tpp) cc_final: 0.7528 (tmm) REVERT: C 158 ASN cc_start: 0.7100 (t0) cc_final: 0.6793 (t0) REVERT: C 250 GLU cc_start: 0.6481 (mm-30) cc_final: 0.6201 (mm-30) REVERT: F 88 ASP cc_start: 0.8061 (t70) cc_final: 0.7499 (t70) outliers start: 47 outliers final: 44 residues processed: 289 average time/residue: 0.1306 time to fit residues: 60.1342 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 231 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 108 GLU 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 283 LEU Chi-restraints excluded: chain G residue 48 GLN 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 38 MET Chi-restraints excluded: chain H residue 47 THR 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 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 156 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 203 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 231 ASN ** 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 = 0.4267 r_free = 0.4267 target = 0.193350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151874 restraints weight = 29941.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149775 restraints weight = 32910.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151599 restraints weight = 27518.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152504 restraints weight = 15394.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.156212 restraints weight = 13455.433| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3808 r_free = 0.3808 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19285 Z= 0.134 Angle : 0.685 12.187 26295 Z= 0.334 Chirality : 0.051 0.308 2934 Planarity : 0.003 0.043 3316 Dihedral : 11.884 174.079 3127 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.45 % Allowed : 19.31 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2380 helix: 0.72 (0.23), residues: 528 sheet: -0.41 (0.24), residues: 511 loop : -2.19 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.019 0.001 TYR D 240 PHE 0.015 0.001 PHE B 202 TRP 0.022 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19285) covalent geometry : angle 0.68468 / 0.33 (26295) hydrogen bonds : bond 0.03047 / 1.93 ( 534) hydrogen bonds : angle 4.47706 / 3.13 ( 1545) ********************** 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 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5031 (mp) cc_final: 0.4159 (tp) REVERT: A 112 TYR cc_start: 0.4650 (OUTLIER) cc_final: 0.3344 (t80) REVERT: A 142 GLN cc_start: 0.7869 (pp30) cc_final: 0.7169 (pp30) REVERT: A 165 GLN cc_start: 0.4838 (mp10) cc_final: 0.4346 (mp10) REVERT: B 182 MET cc_start: 0.7693 (tpp) cc_final: 0.7292 (tmm) REVERT: C 158 ASN cc_start: 0.7001 (t0) cc_final: 0.6703 (t0) REVERT: C 250 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6129 (mm-30) REVERT: D 292 THR cc_start: 0.9249 (t) cc_final: 0.9042 (t) REVERT: F 88 ASP cc_start: 0.7933 (t70) cc_final: 0.7415 (t70) outliers start: 45 outliers final: 41 residues processed: 287 average time/residue: 0.1278 time to fit residues: 58.4282 Evaluate side-chains 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 B residue 139 VAL 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 231 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 108 GLU Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 48 GLN Chi-restraints excluded: chain G residue 140 GLU 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 38 MET Chi-restraints excluded: chain H residue 47 THR 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 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 193 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 206 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 191 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN C 231 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.191502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146427 restraints weight = 32354.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143630 restraints weight = 24534.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144886 restraints weight = 24604.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145699 restraints weight = 16123.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146535 restraints weight = 13756.884| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19285 Z= 0.171 Angle : 0.724 13.266 26295 Z= 0.351 Chirality : 0.053 0.343 2934 Planarity : 0.004 0.045 3316 Dihedral : 11.910 172.992 3127 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.23 % Allowed : 19.64 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2380 helix: 0.65 (0.23), residues: 528 sheet: -0.43 (0.25), residues: 479 loop : -2.26 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.021 0.001 TYR D 240 PHE 0.015 0.002 PHE E 205 TRP 0.019 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19285) covalent geometry : angle 0.72413 / 0.35 (26295) hydrogen bonds : bond 0.03348 / 2.11 ( 534) hydrogen bonds : angle 4.53219 / 3.17 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3559.40 seconds wall clock time: 62 minutes 12.43 seconds (3732.43 seconds total)