Starting phenix.real_space_refine on Fri Sep 19 01:58:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwu_32873/09_2025/7wwu_32873.cif" } 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-2.0-5805/lib/python3.9/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, 'RNA': 49} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 10, 'rna3p_pyr': 20} Link IDs: {'rna2p': 18, 'rna3p': 31} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.41, per 1000 atoms: 0.23 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: 1.65 Conformation dependent library (CDL) restraints added in 855.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.15 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: 2.86 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5651 1.33 - 1.45: 3255 1.45 - 1.57: 10159 1.57 - 1.69: 97 1.69 - 1.81: 123 Bond restraints: 19285 Sorted by residual: bond pdb=" CA VAL G 206 " pdb=" CB VAL G 206 " ideal model delta sigma weight residual 1.542 1.560 -0.018 1.55e-02 4.16e+03 1.34e+00 bond pdb=" CB ASP F 226 " pdb=" CG ASP F 226 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.62e-02 3.81e+03 9.94e-01 bond pdb=" CA MET A 1 " pdb=" C MET A 1 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.10e-02 2.27e+03 8.88e-01 bond pdb=" CG LEU D 270 " pdb=" CD1 LEU D 270 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.87e-01 ... (remaining 19280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 25667 1.71 - 3.43: 552 3.43 - 5.14: 62 5.14 - 6.86: 13 6.86 - 8.57: 4 Bond angle restraints: 26298 Sorted by residual: angle pdb=" C LEU D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 125.66 132.04 -6.38 1.85e+00 2.92e-01 1.19e+01 angle pdb=" N ILE A 75 " pdb=" CA ILE A 75 " pdb=" C ILE A 75 " ideal model delta sigma weight residual 113.16 108.09 5.07 1.49e+00 4.50e-01 1.16e+01 angle pdb=" C LEU E 107 " pdb=" N GLU E 108 " pdb=" CA GLU E 108 " ideal model delta sigma weight residual 125.66 131.41 -5.75 1.85e+00 2.92e-01 9.66e+00 angle pdb=" CA GLU C 108 " pdb=" CB GLU C 108 " pdb=" CG GLU C 108 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.57e+00 angle pdb=" C ASN E 73 " pdb=" N LYS E 74 " pdb=" CA LYS E 74 " ideal model delta sigma weight residual 121.87 128.15 -6.28 2.24e+00 1.99e-01 7.87e+00 ... (remaining 26293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.79: 10630 26.79 - 53.57: 513 53.57 - 80.36: 97 80.36 - 107.14: 11 107.14 - 133.93: 1 Dihedral angle restraints: 11252 sinusoidal: 4707 harmonic: 6545 Sorted by residual: dihedral pdb=" O4' U M 27 " pdb=" C1' U M 27 " pdb=" N1 U M 27 " pdb=" C2 U M 27 " ideal model delta sinusoidal sigma weight residual 200.00 66.07 133.93 1 1.50e+01 4.44e-03 7.23e+01 dihedral pdb=" CA ARG G 131 " pdb=" C ARG G 131 " pdb=" N ASN G 132 " pdb=" CA ASN G 132 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA TRP G 130 " pdb=" C TRP G 130 " pdb=" N ARG G 131 " pdb=" CA ARG G 131 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 11249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2431 0.054 - 0.108: 429 0.108 - 0.162: 70 0.162 - 0.216: 3 0.216 - 0.270: 1 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CB ILE A 2 " pdb=" CA ILE A 2 " pdb=" CG1 ILE A 2 " pdb=" CG2 ILE A 2 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB THR H 268 " pdb=" CA THR H 268 " pdb=" OG1 THR H 268 " pdb=" CG2 THR H 268 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR G 235 " pdb=" CA THR G 235 " pdb=" OG1 THR G 235 " pdb=" CG2 THR G 235 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2931 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA G 6 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO G 7 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 116 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 117 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 226 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C ASP F 226 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP F 226 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN F 227 " 0.009 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 749 2.71 - 3.26: 18518 3.26 - 3.80: 27265 3.80 - 4.35: 34396 4.35 - 4.90: 58053 Nonbonded interactions: 138981 Sorted by model distance: nonbonded pdb=" OH TYR G 117 " pdb=" O ASP G 161 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 13 " pdb=" OE1 GLU D 93 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN B 184 " pdb=" OG1 THR B 211 " model vdw 2.193 3.040 nonbonded pdb=" O TRP D 130 " pdb=" N ASN D 132 " model vdw 2.214 3.120 nonbonded pdb=" N MET A 1 " pdb=" OE2 GLU A 4 " model vdw 2.220 3.120 ... (remaining 138976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'E' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'F' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'G' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) selection = (chain 'H' and (resid 3 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.06 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.030 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19285 Z= 0.134 Angle : 0.604 8.573 26298 Z= 0.336 Chirality : 0.042 0.270 2934 Planarity : 0.004 0.055 3316 Dihedral : 15.511 133.927 7178 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (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 covalent geometry : bond 0.00276 (19285) covalent geometry : angle 0.60366 (26298) hydrogen bonds : bond 0.12921 ( 534) hydrogen bonds : angle 5.77219 ( 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 : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5183 (OUTLIER) cc_final: 0.4865 (p0) REVERT: A 142 GLN cc_start: 0.7915 (pp30) cc_final: 0.7506 (pp30) REVERT: A 150 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 198 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8043 (ttm) REVERT: F 88 ASP cc_start: 0.7984 (t70) cc_final: 0.7578 (t70) outliers start: 2 outliers final: 1 residues processed: 308 average time/residue: 0.1160 time to fit residues: 56.0077 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 : 0.558 ------------------------------------------------------------------------------- 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: 4.9990 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: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN C 203 GLN D 101 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.190440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143480 restraints weight = 31572.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141204 restraints weight = 25259.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143050 restraints weight = 23498.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143414 restraints weight = 15216.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144954 restraints weight = 13739.152| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19285 Z= 0.224 Angle : 0.653 9.473 26298 Z= 0.350 Chirality : 0.045 0.202 2934 Planarity : 0.004 0.048 3316 Dihedral : 13.439 132.019 3293 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.35 % Favored : 88.60 % Rotamer: Outliers : 1.69 % Allowed : 9.96 % Favored : 88.36 % 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 aren not related in a simple way. whole: -1.90 (0.17), residues: 2380 helix: 0.39 (0.23), residues: 527 sheet: -0.44 (0.24), residues: 484 loop : -2.37 (0.16), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 14 TYR 0.031 0.002 TYR D 240 PHE 0.034 0.002 PHE B 226 TRP 0.020 0.002 TRP D 130 HIS 0.004 0.001 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00520 (19285) covalent geometry : angle 0.65332 (26298) hydrogen bonds : bond 0.04167 ( 534) hydrogen bonds : angle 5.07135 ( 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 293 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.3581 (t80) REVERT: A 142 GLN cc_start: 0.7946 (pp30) cc_final: 0.7264 (pp30) REVERT: A 150 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 165 GLN cc_start: 0.5171 (mp10) cc_final: 0.4716 (mp10) REVERT: C 130 TRP cc_start: 0.6908 (m100) cc_final: 0.6633 (m100) REVERT: C 158 ASN cc_start: 0.7188 (t0) cc_final: 0.6908 (t0) REVERT: E 289 MET cc_start: 0.8124 (ttm) cc_final: 0.7859 (ttm) REVERT: F 88 ASP cc_start: 0.8041 (t70) cc_final: 0.7542 (t70) outliers start: 31 outliers final: 24 residues processed: 279 average time/residue: 0.1220 time to fit residues: 54.0013 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 : 0.646 ------------------------------------------------------------------------------- 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 64 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 300 VAL 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 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 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: 4.9990 chunk 132 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN 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 = 0.4252 r_free = 0.4252 target = 0.192067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135994 restraints weight = 36686.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139174 restraints weight = 21350.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139471 restraints weight = 14029.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.140416 restraints weight = 13785.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140583 restraints weight = 12701.592| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19285 Z= 0.152 Angle : 0.584 7.948 26298 Z= 0.312 Chirality : 0.042 0.167 2934 Planarity : 0.004 0.043 3316 Dihedral : 13.259 129.417 3290 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.74 % Allowed : 13.76 % Favored : 84.49 % 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 aren not related in a simple way. whole: -1.78 (0.17), residues: 2380 helix: 0.50 (0.23), residues: 528 sheet: -0.36 (0.24), residues: 479 loop : -2.29 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 234 TYR 0.025 0.001 TYR D 240 PHE 0.016 0.001 PHE G 271 TRP 0.029 0.002 TRP B 231 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00346 (19285) covalent geometry : angle 0.58365 (26298) hydrogen bonds : bond 0.03459 ( 534) hydrogen bonds : angle 4.77273 ( 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: 32 poor density : 263 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7486 (t80) cc_final: 0.7244 (t80) REVERT: A 107 LYS cc_start: 0.7865 (tppt) cc_final: 0.7611 (tppt) REVERT: A 112 TYR cc_start: 0.4967 (OUTLIER) cc_final: 0.3659 (t80) REVERT: A 142 GLN cc_start: 0.7824 (pp30) cc_final: 0.7203 (pp30) REVERT: A 150 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 165 GLN cc_start: 0.4761 (mp10) cc_final: 0.4340 (mp10) REVERT: B 182 MET cc_start: 0.7715 (tpp) cc_final: 0.7161 (tmm) REVERT: C 103 LEU cc_start: 0.8970 (tp) cc_final: 0.8746 (tp) REVERT: C 158 ASN cc_start: 0.6859 (t0) cc_final: 0.6552 (t0) REVERT: C 250 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6168 (mm-30) REVERT: E 289 MET cc_start: 0.8150 (ttm) cc_final: 0.7731 (ttm) REVERT: F 88 ASP cc_start: 0.8025 (t70) cc_final: 0.7494 (t70) REVERT: G 139 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7823 (pt) outliers start: 32 outliers final: 24 residues processed: 286 average time/residue: 0.1242 time to fit residues: 55.7750 Evaluate side-chains 277 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 158 ASN 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 139 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 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: 8.9990 chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 227 optimal weight: 50.0000 chunk 138 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 288 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 = 0.4239 r_free = 0.4239 target = 0.190921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150231 restraints weight = 29412.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147907 restraints weight = 40190.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150626 restraints weight = 27270.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151046 restraints weight = 16510.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153550 restraints weight = 13882.720| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19285 Z= 0.162 Angle : 0.579 7.173 26298 Z= 0.310 Chirality : 0.042 0.158 2934 Planarity : 0.004 0.040 3316 Dihedral : 13.219 128.418 3290 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 2.34 % Allowed : 16.05 % Favored : 81.61 % 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 aren not related in a simple way. whole: -1.79 (0.17), residues: 2380 helix: 0.67 (0.23), residues: 523 sheet: -0.51 (0.24), residues: 489 loop : -2.33 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 257 TYR 0.024 0.002 TYR D 240 PHE 0.015 0.002 PHE G 271 TRP 0.019 0.001 TRP D 130 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00371 (19285) covalent geometry : angle 0.57915 (26298) hydrogen bonds : bond 0.03418 ( 534) hydrogen bonds : angle 4.67916 ( 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 305 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4867 (mp) cc_final: 0.3539 (mt) REVERT: A 106 PHE cc_start: 0.6361 (t80) cc_final: 0.5634 (t80) REVERT: A 112 TYR cc_start: 0.4852 (OUTLIER) cc_final: 0.3279 (t80) REVERT: A 142 GLN cc_start: 0.7814 (pp30) cc_final: 0.7134 (pp30) REVERT: A 150 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 165 GLN cc_start: 0.5084 (mp10) cc_final: 0.4603 (mp10) REVERT: B 26 MET cc_start: 0.7504 (mmm) cc_final: 0.7283 (mmm) REVERT: C 130 TRP cc_start: 0.6836 (m100) cc_final: 0.6629 (m100) REVERT: C 158 ASN cc_start: 0.6815 (t0) cc_final: 0.6527 (t0) REVERT: C 250 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5998 (mm-30) REVERT: F 88 ASP cc_start: 0.7970 (t70) cc_final: 0.7468 (t70) REVERT: G 139 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7779 (pt) outliers start: 43 outliers final: 30 residues processed: 295 average time/residue: 0.1221 time to fit residues: 56.9748 Evaluate side-chains 283 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 158 ASN 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 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 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 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: 0.8980 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.190760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137526 restraints weight = 36580.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137255 restraints weight = 21221.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138428 restraints weight = 16401.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.139246 restraints weight = 15232.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.139348 restraints weight = 12898.087| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1857 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= 0.161 Angle : 0.604 10.916 26298 Z= 0.318 Chirality : 0.042 0.166 2934 Planarity : 0.004 0.039 3316 Dihedral : 13.184 128.083 3290 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.10 % Allowed : 17.19 % Favored : 79.71 % 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 aren not related in a simple way. whole: -1.73 (0.17), residues: 2380 helix: 0.68 (0.23), residues: 528 sheet: -0.52 (0.24), residues: 491 loop : -2.25 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 133 TYR 0.023 0.001 TYR D 240 PHE 0.017 0.001 PHE B 202 TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00369 (19285) covalent geometry : angle 0.60373 (26298) hydrogen bonds : bond 0.03336 ( 534) hydrogen bonds : angle 4.61377 ( 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 318 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7432 (mptt) cc_final: 0.6493 (mmmt) REVERT: A 66 LEU cc_start: 0.5734 (mp) cc_final: 0.4738 (tp) REVERT: A 112 TYR cc_start: 0.4590 (OUTLIER) cc_final: 0.3523 (t80) REVERT: A 142 GLN cc_start: 0.7617 (pp30) cc_final: 0.6902 (pp30) REVERT: A 150 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 165 GLN cc_start: 0.4584 (mp10) cc_final: 0.4162 (mp10) REVERT: C 158 ASN cc_start: 0.6840 (t0) cc_final: 0.6532 (t0) REVERT: C 250 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6106 (mm-30) REVERT: F 88 ASP cc_start: 0.8080 (t70) cc_final: 0.7510 (t70) REVERT: G 139 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7726 (pt) outliers start: 57 outliers final: 40 residues processed: 305 average time/residue: 0.1198 time to fit residues: 57.7009 Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 62 ILE 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 294 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain G residue 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 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: 0.5980 chunk 91 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN E 294 ASN F 227 GLN G 279 ASN ** H 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.193027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150775 restraints weight = 26849.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.146885 restraints weight = 30262.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149419 restraints weight = 27729.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149822 restraints weight = 16652.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152037 restraints weight = 14801.494| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1982 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= 0.121 Angle : 0.574 9.268 26298 Z= 0.301 Chirality : 0.041 0.176 2934 Planarity : 0.003 0.050 3316 Dihedral : 13.039 127.098 3290 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.50 % Allowed : 18.72 % Favored : 78.78 % 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 aren not related in a simple way. whole: -1.57 (0.17), residues: 2380 helix: 0.88 (0.24), residues: 528 sheet: -0.43 (0.24), residues: 501 loop : -2.19 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 177 TYR 0.018 0.001 TYR D 240 PHE 0.016 0.001 PHE F 205 TRP 0.020 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00270 (19285) covalent geometry : angle 0.57398 (26298) hydrogen bonds : bond 0.02977 ( 534) hydrogen bonds : angle 4.44378 ( 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 310 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4779 (mp) cc_final: 0.3853 (tp) REVERT: A 112 TYR cc_start: 0.4760 (OUTLIER) cc_final: 0.3343 (t80) REVERT: A 142 GLN cc_start: 0.7761 (pp30) cc_final: 0.7043 (pp30) REVERT: A 150 GLN cc_start: 0.8422 (tm-30) cc_final: 0.7957 (tm-30) REVERT: A 165 GLN cc_start: 0.5015 (mp10) cc_final: 0.4513 (mp10) REVERT: C 22 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4742 (tp) REVERT: C 103 LEU cc_start: 0.9112 (tp) cc_final: 0.8860 (tp) REVERT: C 158 ASN cc_start: 0.6961 (t0) cc_final: 0.6663 (t0) REVERT: C 250 GLU cc_start: 0.6283 (mm-30) cc_final: 0.6075 (mm-30) REVERT: C 289 MET cc_start: 0.8479 (mmm) cc_final: 0.8151 (tpt) REVERT: D 292 THR cc_start: 0.9219 (t) cc_final: 0.9005 (t) REVERT: F 88 ASP cc_start: 0.7998 (t70) cc_final: 0.7480 (t70) outliers start: 46 outliers final: 30 residues processed: 296 average time/residue: 0.1238 time to fit residues: 58.1288 Evaluate side-chains 283 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 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 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 197 optimal weight: 5.9990 chunk 161 optimal weight: 0.0770 chunk 226 optimal weight: 40.0000 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 128 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 2.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 GLN F 227 GLN G 279 ASN H 225 HIS H 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.189610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.135281 restraints weight = 36745.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136378 restraints weight = 21039.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136783 restraints weight = 15906.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138001 restraints weight = 15242.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138040 restraints weight = 12852.477| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19285 Z= 0.191 Angle : 0.626 9.122 26298 Z= 0.331 Chirality : 0.043 0.164 2934 Planarity : 0.004 0.049 3316 Dihedral : 13.201 128.362 3290 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.40 % Favored : 88.56 % Rotamer: Outliers : 2.83 % Allowed : 19.42 % Favored : 77.75 % 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 aren not related in a simple way. whole: -1.77 (0.17), residues: 2380 helix: 0.74 (0.23), residues: 522 sheet: -0.60 (0.24), residues: 511 loop : -2.30 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 177 TYR 0.024 0.002 TYR D 240 PHE 0.016 0.002 PHE G 200 TRP 0.016 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00442 (19285) covalent geometry : angle 0.62618 (26298) hydrogen bonds : bond 0.03560 ( 534) hydrogen bonds : angle 4.63634 ( 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 307 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7395 (tppt) REVERT: A 66 LEU cc_start: 0.5630 (mp) cc_final: 0.4745 (tp) REVERT: A 112 TYR cc_start: 0.4728 (OUTLIER) cc_final: 0.3443 (t80) REVERT: A 142 GLN cc_start: 0.7635 (pp30) cc_final: 0.6913 (pp30) REVERT: A 165 GLN cc_start: 0.4600 (mp10) cc_final: 0.4267 (mp10) REVERT: B 26 MET cc_start: 0.8018 (mmm) cc_final: 0.7562 (mmm) REVERT: B 177 ARG cc_start: 0.9317 (mmm160) cc_final: 0.9047 (mmp80) REVERT: B 182 MET cc_start: 0.7784 (tpp) cc_final: 0.7203 (tmm) REVERT: C 22 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4892 (tp) REVERT: C 158 ASN cc_start: 0.7097 (t0) cc_final: 0.6803 (t0) REVERT: D 107 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8000 (mm) REVERT: F 88 ASP cc_start: 0.8079 (t70) cc_final: 0.7510 (t70) outliers start: 52 outliers final: 43 residues processed: 293 average time/residue: 0.1248 time to fit residues: 57.2254 Evaluate side-chains 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS 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 22 LEU 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 202 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 107 LEU 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 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 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 140 GLU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 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: 0.8980 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 0.0870 chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 159 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 227 GLN ** 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 = 0.4272 r_free = 0.4272 target = 0.194109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152612 restraints weight = 29928.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153851 restraints weight = 40063.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155064 restraints weight = 25470.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155899 restraints weight = 15964.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160168 restraints weight = 13393.625| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19285 Z= 0.107 Angle : 0.591 12.810 26298 Z= 0.305 Chirality : 0.041 0.195 2934 Planarity : 0.003 0.040 3316 Dihedral : 12.963 126.733 3290 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.96 % Allowed : 20.35 % Favored : 77.69 % 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 aren not related in a simple way. whole: -1.51 (0.17), residues: 2380 helix: 0.87 (0.23), residues: 528 sheet: -0.32 (0.24), residues: 501 loop : -2.16 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 177 TYR 0.017 0.001 TYR B 52 PHE 0.019 0.001 PHE A 140 TRP 0.022 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00232 (19285) covalent geometry : angle 0.59101 (26298) hydrogen bonds : bond 0.02802 ( 534) hydrogen bonds : angle 4.39269 ( 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 297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4649 (mp) cc_final: 0.3679 (tp) REVERT: A 112 TYR cc_start: 0.4551 (OUTLIER) cc_final: 0.3266 (t80) REVERT: A 142 GLN cc_start: 0.7869 (pp30) cc_final: 0.7209 (pp30) REVERT: A 165 GLN cc_start: 0.5038 (mp10) cc_final: 0.4517 (mp10) REVERT: C 103 LEU cc_start: 0.9093 (tp) cc_final: 0.8844 (tp) REVERT: C 158 ASN cc_start: 0.6823 (t0) cc_final: 0.6560 (t0) REVERT: D 107 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7917 (mm) REVERT: D 292 THR cc_start: 0.9220 (t) cc_final: 0.9007 (t) REVERT: F 88 ASP cc_start: 0.7955 (t70) cc_final: 0.7446 (t70) outliers start: 36 outliers final: 30 residues processed: 286 average time/residue: 0.1199 time to fit residues: 54.5271 Evaluate side-chains 279 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 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: 0.4980 chunk 194 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 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: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 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 = 0.4265 r_free = 0.4265 target = 0.193477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140889 restraints weight = 36775.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140812 restraints weight = 20311.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141362 restraints weight = 16629.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142474 restraints weight = 14190.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143166 restraints weight = 12570.654| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19285 Z= 0.117 Angle : 0.604 12.249 26298 Z= 0.310 Chirality : 0.041 0.174 2934 Planarity : 0.004 0.080 3316 Dihedral : 12.941 126.872 3290 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.18 % Allowed : 20.51 % Favored : 77.31 % 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 aren not related in a simple way. whole: -1.48 (0.17), residues: 2380 helix: 0.89 (0.23), residues: 528 sheet: -0.29 (0.24), residues: 501 loop : -2.13 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 177 TYR 0.017 0.001 TYR B 52 PHE 0.017 0.001 PHE A 140 TRP 0.018 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00263 (19285) covalent geometry : angle 0.60361 (26298) hydrogen bonds : bond 0.02898 ( 534) hydrogen bonds : angle 4.36323 ( 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 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7444 (tppt) REVERT: A 66 LEU cc_start: 0.5493 (mp) cc_final: 0.4554 (tp) REVERT: A 112 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.3411 (t80) REVERT: A 142 GLN cc_start: 0.7788 (pp30) cc_final: 0.7095 (pp30) REVERT: A 165 GLN cc_start: 0.4715 (mp10) cc_final: 0.4242 (mp10) REVERT: C 103 LEU cc_start: 0.9044 (tp) cc_final: 0.8781 (tp) REVERT: C 158 ASN cc_start: 0.6998 (t0) cc_final: 0.6660 (t0) REVERT: D 107 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7905 (mm) REVERT: D 292 THR cc_start: 0.9228 (t) cc_final: 0.9007 (t) REVERT: F 88 ASP cc_start: 0.8069 (t70) cc_final: 0.7506 (t70) REVERT: G 129 LEU cc_start: 0.7944 (tt) cc_final: 0.7539 (tp) REVERT: H 287 ASP cc_start: 0.8214 (p0) cc_final: 0.7697 (p0) outliers start: 40 outliers final: 33 residues processed: 280 average time/residue: 0.1162 time to fit residues: 52.1027 Evaluate side-chains 285 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS 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 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 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 107 LEU 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 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 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: 0.7980 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 29 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 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 = 0.4270 r_free = 0.4270 target = 0.193955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152421 restraints weight = 29954.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153017 restraints weight = 39217.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155039 restraints weight = 24678.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155344 restraints weight = 16071.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159777 restraints weight = 13355.385| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3855 r_free = 0.3855 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3855 r_free = 0.3855 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19285 Z= 0.113 Angle : 0.607 12.658 26298 Z= 0.310 Chirality : 0.041 0.192 2934 Planarity : 0.003 0.040 3316 Dihedral : 12.899 126.723 3290 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 1.96 % Allowed : 20.78 % Favored : 77.26 % 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 aren not related in a simple way. whole: -1.43 (0.17), residues: 2380 helix: 0.94 (0.24), residues: 528 sheet: -0.25 (0.24), residues: 501 loop : -2.12 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.017 0.001 TYR B 52 PHE 0.019 0.001 PHE F 205 TRP 0.019 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00253 (19285) covalent geometry : angle 0.60717 (26298) hydrogen bonds : bond 0.02831 ( 534) hydrogen bonds : angle 4.32822 ( 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 291 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7213 (tppt) REVERT: A 66 LEU cc_start: 0.4660 (mp) cc_final: 0.3728 (tp) REVERT: A 112 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.3239 (t80) REVERT: A 142 GLN cc_start: 0.7881 (pp30) cc_final: 0.7212 (pp30) REVERT: A 165 GLN cc_start: 0.5002 (mp10) cc_final: 0.4481 (mp10) REVERT: B 26 MET cc_start: 0.7237 (mmm) cc_final: 0.6922 (mmm) REVERT: B 177 ARG cc_start: 0.8745 (mmp80) cc_final: 0.8523 (mmp80) REVERT: C 103 LEU cc_start: 0.9086 (tp) cc_final: 0.8827 (tp) REVERT: C 158 ASN cc_start: 0.6727 (t0) cc_final: 0.6503 (t0) REVERT: D 107 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7978 (mm) REVERT: D 292 THR cc_start: 0.9301 (t) cc_final: 0.9094 (t) REVERT: F 88 ASP cc_start: 0.7935 (t70) cc_final: 0.7408 (t70) REVERT: G 129 LEU cc_start: 0.7875 (tt) cc_final: 0.7499 (tp) outliers start: 36 outliers final: 32 residues processed: 279 average time/residue: 0.1181 time to fit residues: 52.6445 Evaluate side-chains 287 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 55 LYS 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 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 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 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: 3.9990 chunk 103 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 91 optimal weight: 0.0770 chunk 131 optimal weight: 0.0060 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN F 227 GLN G 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.194994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148065 restraints weight = 32379.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145662 restraints weight = 25210.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147736 restraints weight = 20872.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148654 restraints weight = 14486.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148925 restraints weight = 13314.030| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19285 Z= 0.107 Angle : 0.598 12.688 26298 Z= 0.305 Chirality : 0.041 0.183 2934 Planarity : 0.003 0.053 3316 Dihedral : 12.827 126.223 3290 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.96 % Allowed : 20.57 % Favored : 77.48 % 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 aren not related in a simple way. whole: -1.40 (0.17), residues: 2380 helix: 0.99 (0.24), residues: 529 sheet: -0.45 (0.24), residues: 521 loop : -2.03 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 133 TYR 0.017 0.001 TYR B 52 PHE 0.016 0.001 PHE A 140 TRP 0.018 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00235 (19285) covalent geometry : angle 0.59758 (26298) hydrogen bonds : bond 0.02715 ( 534) hydrogen bonds : angle 4.26995 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3283.45 seconds wall clock time: 57 minutes 17.25 seconds (3437.25 seconds total)