Starting phenix.real_space_refine on Sat Jul 4 16:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwu_32873/07_2026/7wwu_32873.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4092 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 49 5.49 5 S 67 5.16 5 C 11635 2.51 5 N 3241 2.21 5 O 3872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18864 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1431 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 6, 'TRANS': 172} Chain: "B" Number of atoms: 1924 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} Conformer: "B" Number of residues, atoms: 248, 1919 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 237} bond proxies already assigned to first conformer: 1950 Chain: "C" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2302 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2307 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 293} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 8, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 267 Conformer: "B" Number of residues, atoms: 167, 656 Classifications: {'peptide': 167} Incomplete info: {'backbone_only': 143, 'n_c_alpha_c_only': 10} Link IDs: {'PTRANS': 3, 'TRANS': 163} Unresolved chain links: 1 Unresolved chain link angles: 18 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 9, 'PHE:plan': 8, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 267 bond proxies already assigned to first conformer: 651 Chain: "M" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1015 Classifications: {'DNA': 1, '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: 22 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: 4.51, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 942.1 milliseconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 37 sheets defined 25.1% alpha, 18.0% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 1.85 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: 2.58 Time building geometry restraints manager: 2.10 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: 10555 26.79 - 53.57: 476 53.57 - 80.36: 47 80.36 - 107.14: 11 107.14 - 133.93: 1 Dihedral angle restraints: 11090 sinusoidal: 4545 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 11087 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19285 Z= 0.134 Angle : 0.604 8.573 26298 Z= 0.336 Chirality : 0.042 0.270 2934 Planarity : 0.004 0.055 3316 Dihedral : 14.401 133.927 7016 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2380 helix: 0.47 (0.23), residues: 526 sheet: -0.17 (0.25), residues: 474 loop : -2.25 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 257 TYR 0.026 0.001 TYR D 240 PHE 0.015 0.001 PHE H 150 TRP 0.018 0.001 TRP D 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (19285) covalent geometry : angle 0.60366 / 0.34 (26298) hydrogen bonds : bond 0.12921 / 8.58 ( 534) hydrogen bonds : angle 5.77219 / 4.09 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5183 (OUTLIER) cc_final: 0.4865 (p0) REVERT: A 142 GLN cc_start: 0.7915 (pp30) cc_final: 0.7506 (pp30) REVERT: A 150 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 198 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8044 (ttm) REVERT: F 88 ASP cc_start: 0.7984 (t70) cc_final: 0.7578 (t70) outliers start: 2 outliers final: 1 residues processed: 308 average time/residue: 0.1249 time to fit residues: 61.2736 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 : 0.695 ------------------------------------------------------------------------------- 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... A 28 ASN C 203 GLN G 48 GLN G 63 GLN H 66 ASN H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.190622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143197 restraints weight = 31641.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140500 restraints weight = 25036.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142538 restraints weight = 22468.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142720 restraints weight = 15163.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144826 restraints weight = 13505.647| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19285 Z= 0.224 Angle : 0.653 9.819 26298 Z= 0.350 Chirality : 0.045 0.198 2934 Planarity : 0.004 0.048 3316 Dihedral : 10.407 133.111 3131 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.27 % Favored : 88.69 % Rotamer: Outliers : 1.63 % Allowed : 10.01 % 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 are not related in a simple way. whole: -1.90 (0.17), residues: 2380 helix: 0.40 (0.23), residues: 525 sheet: -0.45 (0.24), residues: 484 loop : -2.37 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 234 TYR 0.032 0.002 TYR D 240 PHE 0.035 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/Z covalent geometry : bond 0.00520 / 0.22 (19285) covalent geometry : angle 0.65333 / 0.35 (26298) hydrogen bonds : bond 0.04105 / 2.61 ( 534) hydrogen bonds : angle 5.07303 / 3.55 ( 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 294 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.5188 (OUTLIER) cc_final: 0.3675 (t80) REVERT: A 142 GLN cc_start: 0.7932 (pp30) cc_final: 0.7345 (pp30) REVERT: A 150 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7986 (tm-30) REVERT: A 165 GLN cc_start: 0.5067 (mp10) cc_final: 0.4625 (mp10) REVERT: C 130 TRP cc_start: 0.6881 (m100) cc_final: 0.6602 (m100) REVERT: C 158 ASN cc_start: 0.7191 (t0) cc_final: 0.6910 (t0) REVERT: E 289 MET cc_start: 0.8125 (ttm) cc_final: 0.7855 (ttm) REVERT: F 88 ASP cc_start: 0.8040 (t70) cc_final: 0.7535 (t70) outliers start: 30 outliers final: 23 residues processed: 280 average time/residue: 0.1254 time to fit residues: 55.6400 Evaluate side-chains 261 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 169 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 13 optimal weight: 0.0020 chunk 197 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN F 227 GLN G 279 ASN H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.194733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141469 restraints weight = 36749.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141154 restraints weight = 20638.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142449 restraints weight = 16142.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143580 restraints weight = 14521.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143669 restraints weight = 12307.188| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19285 Z= 0.114 Angle : 0.559 8.645 26298 Z= 0.297 Chirality : 0.042 0.172 2934 Planarity : 0.003 0.042 3316 Dihedral : 10.047 130.458 3128 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.36 % Allowed : 13.49 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.17), residues: 2380 helix: 0.64 (0.23), residues: 528 sheet: -0.25 (0.24), residues: 479 loop : -2.22 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 133 TYR 0.021 0.001 TYR B 159 PHE 0.016 0.001 PHE B 226 TRP 0.028 0.001 TRP B 231 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (19285) covalent geometry : angle 0.55869 / 0.30 (26298) hydrogen bonds : bond 0.03085 / 1.98 ( 534) hydrogen bonds : angle 4.61681 / 3.23 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5778 (mp) cc_final: 0.4658 (mt) REVERT: A 106 PHE cc_start: 0.7613 (t80) cc_final: 0.6649 (t80) REVERT: A 107 LYS cc_start: 0.7791 (tppt) cc_final: 0.7562 (tppt) REVERT: A 142 GLN cc_start: 0.7715 (pp30) cc_final: 0.7103 (pp30) REVERT: A 150 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 165 GLN cc_start: 0.4630 (mp10) cc_final: 0.4227 (mp10) REVERT: B 63 ARG cc_start: 0.8059 (mmp-170) cc_final: 0.7821 (mmp-170) REVERT: B 182 MET cc_start: 0.7805 (tpp) cc_final: 0.7220 (tmm) REVERT: B 235 GLU cc_start: 0.8835 (tp30) cc_final: 0.8632 (tp30) REVERT: C 103 LEU cc_start: 0.8916 (tp) cc_final: 0.8691 (tp) REVERT: C 158 ASN cc_start: 0.6787 (t0) cc_final: 0.6467 (t0) REVERT: D 191 MET cc_start: 0.7774 (mtm) cc_final: 0.7452 (mtt) REVERT: D 292 THR cc_start: 0.9170 (t) cc_final: 0.8940 (t) REVERT: F 88 ASP cc_start: 0.7991 (t70) cc_final: 0.7686 (t70) outliers start: 25 outliers final: 20 residues processed: 283 average time/residue: 0.1278 time to fit residues: 57.4462 Evaluate side-chains 272 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 72 HIS Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain H residue 26 VAL 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: 9.9990 chunk 155 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 223 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 227 optimal weight: 50.0000 chunk 138 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 227 GLN G 279 ASN ** 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 = 0.4239 r_free = 0.4239 target = 0.190823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149799 restraints weight = 29332.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.148782 restraints weight = 38961.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150187 restraints weight = 28794.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151483 restraints weight = 16628.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153468 restraints weight = 13778.141| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1671 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= 0.179 Angle : 0.589 7.044 26298 Z= 0.316 Chirality : 0.043 0.163 2934 Planarity : 0.004 0.042 3316 Dihedral : 10.196 130.289 3128 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.02 % Favored : 88.94 % Rotamer: Outliers : 2.23 % Allowed : 15.61 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.17), residues: 2380 helix: 0.72 (0.23), residues: 523 sheet: -0.51 (0.24), residues: 499 loop : -2.27 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 257 TYR 0.026 0.002 TYR D 240 PHE 0.017 0.002 PHE D 67 TRP 0.017 0.002 TRP D 130 HIS 0.003 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (19285) covalent geometry : angle 0.58934 / 0.32 (26298) hydrogen bonds : bond 0.03555 / 2.26 ( 534) hydrogen bonds : angle 4.66723 / 3.27 ( 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 295 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.5474 (p0) cc_final: 0.4957 (p0) REVERT: A 66 LEU cc_start: 0.4811 (mp) cc_final: 0.3492 (mt) REVERT: A 112 TYR cc_start: 0.4715 (OUTLIER) cc_final: 0.3438 (t80) REVERT: A 142 GLN cc_start: 0.7827 (pp30) cc_final: 0.7159 (pp30) REVERT: A 150 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 165 GLN cc_start: 0.5234 (mp10) cc_final: 0.4720 (mp10) REVERT: B 26 MET cc_start: 0.7448 (mmm) cc_final: 0.7011 (mmm) REVERT: C 130 TRP cc_start: 0.6801 (m100) cc_final: 0.6571 (m100) REVERT: C 158 ASN cc_start: 0.6848 (t0) cc_final: 0.6551 (t0) REVERT: C 250 GLU cc_start: 0.6295 (mm-30) cc_final: 0.5911 (mm-30) REVERT: F 88 ASP cc_start: 0.7970 (t70) cc_final: 0.7672 (t70) REVERT: G 139 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7873 (pt) outliers start: 41 outliers final: 28 residues processed: 285 average time/residue: 0.1251 time to fit residues: 56.8017 Evaluate side-chains 275 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 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 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 258 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 211 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN B 228 GLN C 203 GLN E 294 ASN F 227 GLN G 279 ASN H 288 GLN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.194920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141297 restraints weight = 36641.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141840 restraints weight = 21177.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143279 restraints weight = 14356.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144254 restraints weight = 13442.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144662 restraints weight = 12122.988| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19285 Z= 0.103 Angle : 0.556 11.461 26298 Z= 0.292 Chirality : 0.041 0.163 2934 Planarity : 0.003 0.038 3316 Dihedral : 9.872 128.823 3128 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.39 % Allowed : 17.03 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.17), residues: 2380 helix: 0.91 (0.24), residues: 528 sheet: -0.27 (0.24), residues: 499 loop : -2.14 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 257 TYR 0.017 0.001 TYR B 52 PHE 0.018 0.001 PHE B 202 TRP 0.021 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (19285) covalent geometry : angle 0.55556 / 0.29 (26298) hydrogen bonds : bond 0.02766 / 1.77 ( 534) hydrogen bonds : angle 4.40198 / 3.08 ( 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 315 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.5453 (mp) cc_final: 0.4377 (tp) REVERT: A 112 TYR cc_start: 0.4823 (OUTLIER) cc_final: 0.3401 (t80) REVERT: A 142 GLN cc_start: 0.7692 (pp30) cc_final: 0.6997 (pp30) REVERT: A 150 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 165 GLN cc_start: 0.4740 (mp10) cc_final: 0.4284 (mp10) REVERT: C 103 LEU cc_start: 0.9064 (tp) cc_final: 0.8812 (tp) REVERT: C 158 ASN cc_start: 0.6832 (t0) cc_final: 0.6509 (t0) REVERT: C 250 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6082 (mm-30) REVERT: D 292 THR cc_start: 0.9183 (t) cc_final: 0.8971 (t) REVERT: D 294 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8391 (t0) REVERT: F 88 ASP cc_start: 0.8007 (t70) cc_final: 0.7665 (t70) REVERT: G 139 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7844 (pt) REVERT: G 244 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7380 (p) REVERT: H 150 PHE cc_start: 0.7380 (m-80) cc_final: 0.7125 (m-80) outliers start: 44 outliers final: 26 residues processed: 301 average time/residue: 0.1222 time to fit residues: 59.0012 Evaluate side-chains 284 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 63 GLN 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 283 LEU Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 171 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 174 optimal weight: 0.0370 chunk 195 optimal weight: 6.9990 chunk 71 optimal weight: 0.0060 chunk 185 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.195177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153432 restraints weight = 26848.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151966 restraints weight = 32198.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153808 restraints weight = 27435.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154484 restraints weight = 16340.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156818 restraints weight = 14295.288| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19285 Z= 0.107 Angle : 0.562 11.220 26298 Z= 0.293 Chirality : 0.041 0.155 2934 Planarity : 0.003 0.059 3316 Dihedral : 9.769 128.707 3128 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.29 % Allowed : 18.44 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2380 helix: 1.02 (0.24), residues: 528 sheet: -0.45 (0.24), residues: 519 loop : -2.05 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 177 TYR 0.018 0.001 TYR B 52 PHE 0.016 0.001 PHE B 202 TRP 0.018 0.001 TRP D 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (19285) covalent geometry : angle 0.56247 / 0.29 (26298) hydrogen bonds : bond 0.02786 / 1.77 ( 534) hydrogen bonds : angle 4.29424 / 3.01 ( 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 305 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4494 (mp) cc_final: 0.3576 (tp) REVERT: A 106 PHE cc_start: 0.6070 (t80) cc_final: 0.5075 (t80) REVERT: A 112 TYR cc_start: 0.4647 (OUTLIER) cc_final: 0.3172 (t80) REVERT: A 142 GLN cc_start: 0.7777 (pp30) cc_final: 0.7118 (pp30) REVERT: A 150 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 165 GLN cc_start: 0.5004 (mp10) cc_final: 0.4524 (mp10) REVERT: B 26 MET cc_start: 0.6992 (mmm) cc_final: 0.6683 (mmm) REVERT: C 103 LEU cc_start: 0.9099 (tp) cc_final: 0.8828 (tp) REVERT: C 158 ASN cc_start: 0.6935 (t0) cc_final: 0.6634 (t0) REVERT: C 250 GLU cc_start: 0.6293 (mm-30) cc_final: 0.6056 (mm-30) REVERT: D 292 THR cc_start: 0.9186 (t) cc_final: 0.8974 (t) REVERT: F 88 ASP cc_start: 0.7946 (t70) cc_final: 0.7626 (t70) REVERT: G 235 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7444 (t) outliers start: 42 outliers final: 28 residues processed: 294 average time/residue: 0.1160 time to fit residues: 54.6611 Evaluate side-chains 288 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 115 ASP Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 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 235 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 258 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 197 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 226 optimal weight: 50.0000 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 overall best weight: 1.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 203 GLN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.191751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146408 restraints weight = 36806.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145563 restraints weight = 29006.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146403 restraints weight = 28060.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147268 restraints weight = 17444.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149492 restraints weight = 15055.367| |-----------------------------------------------------------------------------| 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 = 0.02 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 = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19285 Z= 0.149 Angle : 0.598 10.264 26298 Z= 0.313 Chirality : 0.042 0.209 2934 Planarity : 0.004 0.047 3316 Dihedral : 9.911 129.618 3128 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.18 % Allowed : 19.10 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2380 helix: 0.99 (0.24), residues: 523 sheet: -0.38 (0.24), residues: 511 loop : -2.20 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 177 TYR 0.021 0.001 TYR D 240 PHE 0.016 0.001 PHE B 202 TRP 0.017 0.001 TRP D 130 HIS 0.003 0.001 HIS F 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (19285) covalent geometry : angle 0.59781 / 0.31 (26298) hydrogen bonds : bond 0.03212 / 2.04 ( 534) hydrogen bonds : angle 4.38337 / 3.07 ( 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 299 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.4774 (mp) cc_final: 0.3875 (tp) REVERT: A 112 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.3605 (t80) REVERT: A 142 GLN cc_start: 0.7764 (pp30) cc_final: 0.7058 (pp30) REVERT: A 150 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 165 GLN cc_start: 0.5037 (mp10) cc_final: 0.4526 (mp10) REVERT: B 26 MET cc_start: 0.7322 (mmm) cc_final: 0.6808 (mmm) REVERT: C 130 TRP cc_start: 0.6674 (m100) cc_final: 0.6432 (m100) REVERT: C 158 ASN cc_start: 0.7025 (t0) cc_final: 0.6715 (t0) REVERT: C 250 GLU cc_start: 0.6378 (mm-30) cc_final: 0.6150 (mm-30) REVERT: D 191 MET cc_start: 0.7910 (mtm) cc_final: 0.7536 (mtt) REVERT: D 289 MET cc_start: 0.7627 (mtm) cc_final: 0.7360 (mtm) REVERT: D 292 THR cc_start: 0.9243 (t) cc_final: 0.9031 (t) REVERT: F 88 ASP cc_start: 0.8032 (t70) cc_final: 0.7707 (t70) outliers start: 40 outliers final: 28 residues processed: 287 average time/residue: 0.1154 time to fit residues: 53.0091 Evaluate side-chains 281 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 252 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.6022 > 50: distance: 88 - 94: 16.685 distance: 94 - 95: 7.441 distance: 95 - 96: 7.637 distance: 95 - 98: 19.669 distance: 96 - 102: 24.898 distance: 98 - 99: 7.755 distance: 99 - 100: 18.591 distance: 99 - 101: 14.499 distance: 102 - 103: 44.580 distance: 103 - 104: 39.100 distance: 103 - 106: 32.105 distance: 104 - 105: 29.460 distance: 104 - 110: 21.635 distance: 106 - 107: 51.096 distance: 107 - 108: 52.638 distance: 107 - 109: 46.898 distance: 110 - 111: 31.239 distance: 111 - 112: 40.669 distance: 112 - 113: 23.379 distance: 112 - 114: 23.072 distance: 114 - 115: 54.043 distance: 115 - 116: 41.809 distance: 115 - 118: 10.480 distance: 116 - 117: 44.079 distance: 116 - 123: 41.812 distance: 118 - 119: 27.513 distance: 119 - 120: 25.152 distance: 120 - 121: 10.446 distance: 120 - 122: 16.001 distance: 123 - 124: 29.231 distance: 124 - 125: 54.787 distance: 125 - 126: 32.998 distance: 125 - 127: 26.107 distance: 127 - 128: 6.903 distance: 128 - 129: 11.897 distance: 128 - 131: 17.242 distance: 129 - 130: 13.045 distance: 129 - 133: 15.737 distance: 131 - 132: 35.296 distance: 133 - 134: 13.281 distance: 134 - 135: 4.124 distance: 134 - 137: 23.731 distance: 135 - 136: 19.768 distance: 135 - 142: 24.372 distance: 137 - 138: 10.880 distance: 138 - 139: 12.056 distance: 139 - 140: 11.838 distance: 139 - 141: 32.667 distance: 142 - 143: 30.131 distance: 143 - 144: 14.803 distance: 143 - 146: 20.916 distance: 144 - 145: 28.916 distance: 144 - 149: 28.174 distance: 146 - 147: 7.255 distance: 146 - 148: 32.643 distance: 149 - 150: 10.535 distance: 150 - 151: 29.507 distance: 150 - 153: 10.356 distance: 151 - 152: 18.223 distance: 151 - 160: 31.569 distance: 153 - 154: 13.215 distance: 154 - 155: 10.787 distance: 154 - 156: 11.376 distance: 155 - 157: 15.585 distance: 156 - 158: 9.087 distance: 157 - 159: 9.330 distance: 158 - 159: 8.953 distance: 160 - 161: 24.242 distance: 160 - 166: 13.550 distance: 161 - 162: 28.553 distance: 161 - 164: 19.676 distance: 162 - 163: 39.844 distance: 162 - 167: 22.990 distance: 164 - 165: 20.785 distance: 165 - 166: 30.957