Starting phenix.real_space_refine on Sat Sep 12 23:32:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b46_7050/09_2026/6b46_7050.map" } resolution = 3.1 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= 0.056 sd= 1.082 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 1240 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 59 5.49 5 S 18 5.16 5 C 11200 2.51 5 N 3374 2.21 5 O 3693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18344 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "J" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 758 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 806 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.99, per 1000 atoms: 0.22 Number of scatterers: 18344 At special positions: 0 Unit cell: (127.937, 122.985, 151.048, 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 18 16.00 P 59 15.00 O 3693 8.00 N 3374 7.00 C 11200 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: 1.52 Conformation dependent library (CDL) restraints added in 846.0 milliseconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3932 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 38 sheets defined 29.0% alpha, 20.6% beta 1 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.738A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 129 removed outlier: 3.863A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.633A pdb=" N GLY C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.595A pdb=" N ALA D 35 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 32 through 36' Processing helix chain 'D' and resid 65 through 73 removed outlier: 5.453A pdb=" N ILE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.511A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.766A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.502A pdb=" N GLN E 129 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 189 through 205 Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.832A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 285 No H-bonds generated for 'chain 'E' and resid 283 through 285' Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.578A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 72 Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.700A pdb=" N GLN F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 205 Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.679A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG F 265 " --> pdb=" O GLY F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 312 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.503A pdb=" N LEU G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.689A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 292 Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 63 through 72 Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 189 through 204 removed outlier: 3.740A pdb=" N SER H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 304 through 313 removed outlier: 3.638A pdb=" N LEU H 313 " --> pdb=" O ASP H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.713A pdb=" N GLN H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 Processing helix chain 'I' and resid 61 through 73 Processing helix chain 'J' and resid 46 through 55 Processing helix chain 'J' and resid 61 through 73 Processing helix chain 'L' and resid 16 through 32 Processing helix chain 'L' and resid 63 through 69 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'C' and resid 108 through 109 removed outlier: 3.645A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.503A pdb=" N VAL C 93 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 210 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 172 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.826A pdb=" N ARG C 94 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 23 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 255 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 252 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA5, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.255A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.515A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.217A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.518A pdb=" N ILE D 255 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 252 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 51 removed outlier: 3.925A pdb=" N GLY D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 75 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB2, first strand: chain 'D' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.675A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.355A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.843A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 252 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 50 removed outlier: 3.572A pdb=" N VAL E 81 " --> pdb=" O ARG E 45 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AB8, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AB9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.545A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.507A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE F 162 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.691A pdb=" N VAL F 49 " --> pdb=" O GLN F 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.979A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.550A pdb=" N ARG G 94 " --> pdb=" O LEU G 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.193A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 50 Processing sheet with id=AC9, first strand: chain 'G' and resid 229 through 230 removed outlier: 4.711A pdb=" N THR G 245 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 248 through 249 removed outlier: 3.571A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD3, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'H' and resid 12 through 14 removed outlier: 4.073A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE H 336 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 20 removed outlier: 4.484A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 170 through 173 removed outlier: 6.718A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 23 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 252 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.818A pdb=" N VAL H 81 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS H 47 " --> pdb=" O VAL H 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.870A pdb=" N ASP H 268 " --> pdb=" O ILE H 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 2 through 6 removed outlier: 3.700A pdb=" N LYS I 2 " --> pdb=" O GLU I 21 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL I 19 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR I 6 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE I 17 " --> pdb=" O TYR I 6 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY I 40 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN I 32 " --> pdb=" O SER I 38 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER I 38 " --> pdb=" O ASN I 32 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 2 through 6 removed outlier: 3.700A pdb=" N LYS J 2 " --> pdb=" O GLU J 21 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL J 19 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR J 6 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE J 17 " --> pdb=" O TYR J 6 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY J 40 " --> pdb=" O VAL J 30 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN J 32 " --> pdb=" O SER J 38 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER J 38 " --> pdb=" O ASN J 32 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 5 through 7 741 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4999 1.33 - 1.45: 3492 1.45 - 1.57: 10152 1.57 - 1.68: 118 1.68 - 1.80: 30 Bond restraints: 18791 Sorted by residual: bond pdb=" C PHE L 158 " pdb=" N ILE L 159 " ideal model delta sigma weight residual 1.332 1.312 0.020 5.60e-03 3.19e+04 1.21e+01 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.446 0.067 3.90e-02 6.57e+02 2.96e+00 bond pdb=" CG1 ILE F 260 " pdb=" CD1 ILE F 260 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.24e+00 bond pdb=" CB TRP G 270 " pdb=" CG TRP G 270 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.21e+00 bond pdb=" CG1 ILE F 267 " pdb=" CD1 ILE F 267 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 ... (remaining 18786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 25005 2.54 - 5.09: 617 5.09 - 7.63: 56 7.63 - 10.17: 13 10.17 - 12.72: 2 Bond angle restraints: 25693 Sorted by residual: angle pdb=" C ARG F 296 " pdb=" N GLN F 297 " pdb=" CA GLN F 297 " ideal model delta sigma weight residual 120.49 129.77 -9.28 1.42e+00 4.96e-01 4.27e+01 angle pdb=" C ARG H 250 " pdb=" N ASP H 251 " pdb=" CA ASP H 251 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C LYS G 58 " pdb=" N THR G 59 " pdb=" CA THR G 59 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C LYS E 238 " pdb=" N LYS E 239 " pdb=" CA LYS E 239 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CA GLN D 241 " pdb=" CB GLN D 241 " pdb=" CG GLN D 241 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.50e+01 ... (remaining 25688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 10091 16.54 - 33.08: 536 33.08 - 49.62: 127 49.62 - 66.16: 94 66.16 - 82.70: 32 Dihedral angle restraints: 10880 sinusoidal: 4589 harmonic: 6291 Sorted by residual: dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.34 -37.56 73.91 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' C M 13 " pdb=" C3' C M 13 " pdb=" C2' C M 13 " pdb=" C1' C M 13 " ideal model delta sinusoidal sigma weight residual 36.34 -37.44 73.79 1 3.10e+00 1.04e-01 7.20e+02 dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -37.09 73.43 1 3.10e+00 1.04e-01 7.14e+02 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2619 0.115 - 0.231: 131 0.231 - 0.346: 68 0.346 - 0.462: 0 0.462 - 0.577: 1 Chirality restraints: 2819 Sorted by residual: chirality pdb=" C1' C M 1 " pdb=" O4' C M 1 " pdb=" C2' C M 1 " pdb=" N1 C M 1 " both_signs ideal model delta sigma weight residual False 2.46 1.88 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" C2' C M 13 " pdb=" C3' C M 13 " pdb=" O2' C M 13 " pdb=" C1' C M 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C2' C M 38 " pdb=" C3' C M 38 " pdb=" O2' C M 38 " pdb=" C1' C M 38 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2816 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " 0.019 2.00e-02 2.50e+03 1.78e-02 7.88e+00 pdb=" CG TRP D 311 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A M 12 " -0.035 2.00e-02 2.50e+03 1.67e-02 7.68e+00 pdb=" N9 A M 12 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A M 12 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A M 12 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A M 12 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A M 12 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A M 12 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A M 12 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A M 12 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 297 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO E 298 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " 0.034 5.00e-02 4.00e+02 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5304 2.82 - 3.34: 15175 3.34 - 3.86: 29758 3.86 - 4.38: 34352 4.38 - 4.90: 58550 Nonbonded interactions: 143139 Sorted by model distance: nonbonded pdb=" OE2 GLU E 283 " pdb=" OG SER E 287 " model vdw 2.296 3.040 nonbonded pdb=" O SER C 36 " pdb=" NZ LYS C 92 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS F 259 " pdb=" OP1 U M 22 " model vdw 2.312 3.120 nonbonded pdb=" OD1 ASP C 22 " pdb=" OG SER C 257 " model vdw 2.330 3.040 nonbonded pdb=" OG SER H 287 " pdb=" O LYS H 293 " model vdw 2.340 3.040 ... (remaining 143134 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' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.430 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.006 0.067 18791 Z= 0.262 Angle : 0.927 12.715 25693 Z= 0.499 Chirality : 0.070 0.577 2819 Planarity : 0.006 0.063 3213 Dihedral : 13.365 82.697 6948 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.47 % Rotamer: Outliers : 0.18 % Allowed : 1.39 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.95 (0.14), residues: 2286 helix: -2.42 (0.15), residues: 652 sheet: -1.60 (0.25), residues: 415 loop : -3.20 (0.14), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 146 TYR 0.035 0.004 TYR F 138 PHE 0.028 0.003 PHE E 336 TRP 0.047 0.005 TRP D 311 HIS 0.019 0.004 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (18791) covalent geometry : angle 0.92726 / 0.50 (25693) hydrogen bonds : bond 0.20130 / 12.90 ( 716) hydrogen bonds : angle 8.16509 / 5.91 ( 2055) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 270 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 LEU cc_start: 0.7023 (mm) cc_final: 0.6776 (tp) REVERT: C 250 ARG cc_start: 0.6832 (ptt180) cc_final: 0.6500 (ptp-110) REVERT: C 277 LEU cc_start: 0.6566 (mp) cc_final: 0.6344 (mp) REVERT: D 45 ARG cc_start: 0.7553 (mtm110) cc_final: 0.7306 (mtm-85) REVERT: H 34 ASP cc_start: 0.7005 (m-30) cc_final: 0.6656 (t0) REVERT: I 9 THR cc_start: 0.8795 (m) cc_final: 0.8490 (t) outliers start: 3 outliers final: 1 residues processed: 272 average time/residue: 0.1868 time to fit residues: 70.3468 Evaluate side-chains 145 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN C 129 GLN C 164 HIS D 129 GLN E 208 HIS F 241 GLN F 291 GLN G 129 GLN H 151 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.150929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117673 restraints weight = 30998.384| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.76 r_work: 0.3367 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18791 Z= 0.199 Angle : 0.897 20.918 25693 Z= 0.409 Chirality : 0.073 0.833 2819 Planarity : 0.005 0.063 3213 Dihedral : 11.653 139.348 3229 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 1.27 % Allowed : 5.49 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.72 (0.16), residues: 2286 helix: -0.60 (0.19), residues: 661 sheet: -0.68 (0.26), residues: 390 loop : -3.01 (0.14), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 175 TYR 0.016 0.002 TYR E 305 PHE 0.020 0.002 PHE J 44 TRP 0.026 0.002 TRP D 311 HIS 0.010 0.002 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (18791) covalent geometry : angle 0.89661 / 0.41 (25693) hydrogen bonds : bond 0.04378 / 2.86 ( 716) hydrogen bonds : angle 5.44963 / 3.89 ( 2055) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.7351 (t0) REVERT: C 136 ARG cc_start: 0.8115 (ttp-110) cc_final: 0.7884 (mtm-85) REVERT: C 259 LYS cc_start: 0.8276 (tttt) cc_final: 0.7929 (tttp) REVERT: C 277 LEU cc_start: 0.6347 (mp) cc_final: 0.6120 (mp) REVERT: D 45 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7639 (mtm-85) REVERT: D 187 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7652 (mtmm) REVERT: F 228 SER cc_start: 0.8804 (p) cc_final: 0.8517 (m) REVERT: G 60 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (pttt) REVERT: H 34 ASP cc_start: 0.6877 (m-30) cc_final: 0.6513 (t0) REVERT: H 212 GLU cc_start: 0.7595 (pp20) cc_final: 0.7243 (pp20) REVERT: H 321 GLU cc_start: 0.7013 (mp0) cc_final: 0.6333 (mt-10) REVERT: J 31 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7583 (mt-10) outliers start: 21 outliers final: 11 residues processed: 176 average time/residue: 0.1774 time to fit residues: 45.0571 Evaluate side-chains 153 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 172 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 225 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 183 optimal weight: 0.0370 overall best weight: 3.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN D 164 HIS F 241 GLN ** H 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.150709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116456 restraints weight = 31456.002| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.69 r_work: 0.3363 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18791 Z= 0.172 Angle : 0.730 13.212 25693 Z= 0.350 Chirality : 0.057 0.386 2819 Planarity : 0.004 0.061 3213 Dihedral : 12.032 163.978 3229 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.93 % Allowed : 7.00 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.17), residues: 2286 helix: 0.33 (0.20), residues: 658 sheet: -0.49 (0.27), residues: 412 loop : -2.76 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 115 TYR 0.016 0.002 TYR E 305 PHE 0.024 0.002 PHE J 44 TRP 0.019 0.002 TRP D 311 HIS 0.008 0.002 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (18791) covalent geometry : angle 0.73028 / 0.35 (25693) hydrogen bonds : bond 0.03816 / 2.50 ( 716) hydrogen bonds : angle 4.92835 / 3.50 ( 2055) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7113 (mm-30) REVERT: C 277 LEU cc_start: 0.6252 (mp) cc_final: 0.6001 (mp) REVERT: D 45 ARG cc_start: 0.8221 (mtm110) cc_final: 0.7896 (mtm-85) REVERT: F 32 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: G 60 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8411 (pttt) REVERT: H 321 GLU cc_start: 0.6964 (mp0) cc_final: 0.6344 (mt-10) REVERT: H 325 TYR cc_start: 0.7219 (t80) cc_final: 0.6968 (t80) REVERT: I 25 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7779 (pttt) REVERT: I 39 VAL cc_start: 0.8331 (m) cc_final: 0.8073 (p) REVERT: J 52 SER cc_start: 0.8628 (p) cc_final: 0.8425 (p) outliers start: 32 outliers final: 20 residues processed: 166 average time/residue: 0.1658 time to fit residues: 40.7152 Evaluate side-chains 156 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 182 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN H 323 GLN I 49 GLN ** J 49 GLN ** 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 = 0.3949 r_free = 0.3949 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113170 restraints weight = 31549.257| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.45 r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18791 Z= 0.207 Angle : 0.749 11.662 25693 Z= 0.360 Chirality : 0.057 0.451 2819 Planarity : 0.005 0.060 3213 Dihedral : 12.009 162.260 3229 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.35 % Allowed : 7.91 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.80 (0.17), residues: 2286 helix: 0.64 (0.21), residues: 658 sheet: -0.50 (0.27), residues: 403 loop : -2.62 (0.15), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 136 TYR 0.018 0.002 TYR G 285 PHE 0.011 0.002 PHE F 336 TRP 0.017 0.002 TRP E 311 HIS 0.007 0.002 HIS E 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (18791) covalent geometry : angle 0.74922 / 0.36 (25693) hydrogen bonds : bond 0.03921 / 2.57 ( 716) hydrogen bonds : angle 4.89036 / 3.47 ( 2055) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 GLN cc_start: 0.0055 (OUTLIER) cc_final: -0.0614 (tp40) REVERT: C 230 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7088 (mm-30) REVERT: C 277 LEU cc_start: 0.6342 (mp) cc_final: 0.6101 (mp) REVERT: D 45 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7945 (mtm-85) REVERT: E 119 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7604 (mm) REVERT: F 32 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: G 60 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8453 (pttt) REVERT: G 114 TYR cc_start: 0.7673 (t80) cc_final: 0.7385 (t80) REVERT: H 224 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: H 321 GLU cc_start: 0.6967 (mp0) cc_final: 0.6633 (mt-10) REVERT: H 323 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5614 (mp-120) REVERT: H 332 ARG cc_start: 0.5387 (tmt-80) cc_final: 0.4466 (tmt-80) REVERT: I 39 VAL cc_start: 0.8341 (m) cc_final: 0.8044 (p) REVERT: J 71 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6949 (tm-30) outliers start: 39 outliers final: 24 residues processed: 170 average time/residue: 0.1785 time to fit residues: 44.3269 Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 60 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 323 GLN Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 64 optimal weight: 9.9990 chunk 215 optimal weight: 50.0000 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 221 optimal weight: 50.0000 chunk 126 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** G 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** J 49 GLN ** 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 = 0.3974 r_free = 0.3974 target = 0.150789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115525 restraints weight = 31232.221| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.44 r_work: 0.3370 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18791 Z= 0.144 Angle : 0.677 11.766 25693 Z= 0.326 Chirality : 0.052 0.349 2819 Planarity : 0.004 0.056 3213 Dihedral : 11.860 167.675 3229 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.93 % Allowed : 9.41 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.17), residues: 2286 helix: 0.94 (0.21), residues: 658 sheet: -0.25 (0.27), residues: 415 loop : -2.53 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 136 TYR 0.018 0.002 TYR C 295 PHE 0.020 0.001 PHE J 44 TRP 0.012 0.001 TRP H 174 HIS 0.011 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (18791) covalent geometry : angle 0.67659 / 0.33 (25693) hydrogen bonds : bond 0.03357 / 2.20 ( 716) hydrogen bonds : angle 4.63479 / 3.28 ( 2055) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8795 (mtp) cc_final: 0.8499 (mtt) REVERT: C 230 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7020 (mm-30) REVERT: C 277 LEU cc_start: 0.6343 (mp) cc_final: 0.6110 (mp) REVERT: D 45 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7865 (mtm-85) REVERT: E 119 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7567 (mm) REVERT: F 32 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: G 114 TYR cc_start: 0.7630 (t80) cc_final: 0.7423 (t80) REVERT: H 174 TRP cc_start: 0.7134 (m-90) cc_final: 0.6300 (m-90) REVERT: H 224 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6320 (tp30) REVERT: I 39 VAL cc_start: 0.8340 (m) cc_final: 0.8019 (p) REVERT: I 71 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7946 (tm-30) outliers start: 32 outliers final: 22 residues processed: 163 average time/residue: 0.1736 time to fit residues: 41.4605 Evaluate side-chains 153 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 97 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 171 optimal weight: 0.3980 chunk 121 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.147725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113487 restraints weight = 31230.340| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.81 r_work: 0.3319 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18791 Z= 0.226 Angle : 0.756 11.369 25693 Z= 0.365 Chirality : 0.057 0.461 2819 Planarity : 0.005 0.055 3213 Dihedral : 12.085 171.844 3229 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.35 % Allowed : 10.02 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.17), residues: 2286 helix: 0.87 (0.21), residues: 656 sheet: -0.25 (0.28), residues: 407 loop : -2.49 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 115 TYR 0.016 0.002 TYR H 114 PHE 0.011 0.002 PHE C 147 TRP 0.016 0.002 TRP E 311 HIS 0.006 0.002 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 (18791) covalent geometry : angle 0.75554 / 0.36 (25693) hydrogen bonds : bond 0.03995 / 2.62 ( 716) hydrogen bonds : angle 4.83944 / 3.41 ( 2055) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8800 (mtp) cc_final: 0.8515 (mtt) REVERT: C 230 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7126 (mm-30) REVERT: D 45 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7846 (mtm-85) REVERT: E 119 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7654 (mm) REVERT: F 32 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: G 140 HIS cc_start: 0.8274 (OUTLIER) cc_final: 0.7905 (t-90) REVERT: H 224 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6498 (tp30) REVERT: H 321 GLU cc_start: 0.6874 (mp0) cc_final: 0.6486 (mt-10) REVERT: I 39 VAL cc_start: 0.8369 (m) cc_final: 0.8046 (p) outliers start: 39 outliers final: 30 residues processed: 167 average time/residue: 0.1609 time to fit residues: 39.6862 Evaluate side-chains 169 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 203 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN F 241 GLN I 49 GLN ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119384 restraints weight = 31396.982| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.45 r_work: 0.3425 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18791 Z= 0.098 Angle : 0.617 12.250 25693 Z= 0.296 Chirality : 0.048 0.334 2819 Planarity : 0.003 0.053 3213 Dihedral : 11.649 179.883 3229 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.99 % Allowed : 10.92 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.17), residues: 2286 helix: 1.25 (0.21), residues: 659 sheet: -0.09 (0.28), residues: 409 loop : -2.39 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.018 0.001 TYR G 247 PHE 0.009 0.001 PHE C 147 TRP 0.014 0.001 TRP C 174 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (18791) covalent geometry : angle 0.61708 / 0.30 (25693) hydrogen bonds : bond 0.02871 / 1.90 ( 716) hydrogen bonds : angle 4.33849 / 3.06 ( 2055) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8792 (mtp) cc_final: 0.8486 (mtt) REVERT: C 230 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6919 (mm-30) REVERT: D 45 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7749 (mtm-85) REVERT: E 119 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7542 (mm) REVERT: F 32 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: H 83 ASN cc_start: 0.8168 (m-40) cc_final: 0.7138 (m-40) REVERT: H 224 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6119 (tp30) REVERT: H 332 ARG cc_start: 0.5362 (OUTLIER) cc_final: 0.4623 (tmt-80) REVERT: I 71 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7820 (tm-30) outliers start: 33 outliers final: 20 residues processed: 175 average time/residue: 0.1615 time to fit residues: 41.5382 Evaluate side-chains 160 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 73 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 221 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 178 optimal weight: 0.0470 chunk 58 optimal weight: 9.9990 chunk 170 optimal weight: 40.0000 chunk 210 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN H 37 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113078 restraints weight = 31222.043| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.42 r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18791 Z= 0.209 Angle : 0.721 11.621 25693 Z= 0.347 Chirality : 0.054 0.375 2819 Planarity : 0.004 0.056 3213 Dihedral : 11.838 178.110 3229 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.93 % Allowed : 11.41 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.17), residues: 2286 helix: 1.16 (0.21), residues: 657 sheet: -0.10 (0.28), residues: 392 loop : -2.37 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.018 0.002 TYR G 247 PHE 0.012 0.002 PHE C 147 TRP 0.016 0.002 TRP E 311 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (18791) covalent geometry : angle 0.72119 / 0.35 (25693) hydrogen bonds : bond 0.03720 / 2.43 ( 716) hydrogen bonds : angle 4.62187 / 3.24 ( 2055) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 ASP cc_start: 0.7619 (m-30) cc_final: 0.6811 (m-30) REVERT: C 25 MET cc_start: 0.8816 (mtp) cc_final: 0.8526 (mtt) REVERT: C 230 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7096 (mm-30) REVERT: C 259 LYS cc_start: 0.8444 (tttt) cc_final: 0.8144 (tttt) REVERT: D 45 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7871 (mtm-85) REVERT: E 119 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7621 (mm) REVERT: F 32 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8115 (mp10) REVERT: H 224 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: H 321 GLU cc_start: 0.6985 (mp0) cc_final: 0.6605 (mt-10) outliers start: 32 outliers final: 26 residues processed: 160 average time/residue: 0.1592 time to fit residues: 37.7910 Evaluate side-chains 161 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 270 TRP Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 73 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 159 optimal weight: 9.9990 chunk 223 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 161 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 224 optimal weight: 50.0000 chunk 123 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** H 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** 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 = 0.3913 r_free = 0.3913 target = 0.145759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110266 restraints weight = 31106.693| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.36 r_work: 0.3295 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18791 Z= 0.297 Angle : 0.839 11.593 25693 Z= 0.406 Chirality : 0.061 0.544 2819 Planarity : 0.005 0.058 3213 Dihedral : 12.311 177.669 3229 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.17 % Allowed : 11.23 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.17), residues: 2286 helix: 0.78 (0.21), residues: 655 sheet: -0.15 (0.28), residues: 402 loop : -2.54 (0.15), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 146 TYR 0.019 0.003 TYR G 247 PHE 0.013 0.002 PHE C 147 TRP 0.019 0.002 TRP E 311 HIS 0.008 0.002 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.30 (18791) covalent geometry : angle 0.83887 / 0.41 (25693) hydrogen bonds : bond 0.04455 / 2.93 ( 716) hydrogen bonds : angle 4.99263 / 3.50 ( 2055) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8843 (mtp) cc_final: 0.8574 (mtt) REVERT: C 230 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7165 (mm-30) REVERT: C 259 LYS cc_start: 0.8519 (tttt) cc_final: 0.8211 (tttt) REVERT: D 45 ARG cc_start: 0.8190 (mtm110) cc_final: 0.7933 (mtm-85) REVERT: E 119 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7696 (mm) REVERT: F 32 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: G 140 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7572 (t-90) REVERT: H 224 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: H 321 GLU cc_start: 0.6990 (mp0) cc_final: 0.6731 (mt-10) outliers start: 36 outliers final: 27 residues processed: 155 average time/residue: 0.1555 time to fit residues: 36.3641 Evaluate side-chains 157 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 19 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 297 GLN E 72 GLN F 241 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114055 restraints weight = 31199.337| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.76 r_work: 0.3334 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18791 Z= 0.184 Angle : 0.715 11.854 25693 Z= 0.346 Chirality : 0.054 0.411 2819 Planarity : 0.004 0.057 3213 Dihedral : 12.052 177.925 3229 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.81 % Allowed : 11.35 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.17), residues: 2286 helix: 1.01 (0.21), residues: 658 sheet: -0.05 (0.28), residues: 389 loop : -2.45 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.016 0.002 TYR G 247 PHE 0.011 0.001 PHE C 147 TRP 0.012 0.002 TRP E 311 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (18791) covalent geometry : angle 0.71460 / 0.35 (25693) hydrogen bonds : bond 0.03592 / 2.36 ( 716) hydrogen bonds : angle 4.66790 / 3.28 ( 2055) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8855 (mtp) cc_final: 0.8584 (mtt) REVERT: C 230 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7134 (mm-30) REVERT: D 45 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7888 (mtm-85) REVERT: E 119 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7646 (mm) REVERT: F 32 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: H 45 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7390 (mtp-110) REVERT: H 224 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6388 (tp30) REVERT: H 321 GLU cc_start: 0.6940 (mp0) cc_final: 0.6652 (mt-10) REVERT: H 332 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.4638 (tmt-80) outliers start: 30 outliers final: 22 residues processed: 147 average time/residue: 0.1622 time to fit residues: 35.2819 Evaluate side-chains 155 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 ARG Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 224 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 191 optimal weight: 40.0000 chunk 155 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 147 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 241 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 49 GLN ** 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 = 0.3960 r_free = 0.3960 target = 0.149524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115461 restraints weight = 31070.741| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.86 r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18791 Z= 0.156 Angle : 0.679 11.970 25693 Z= 0.328 Chirality : 0.052 0.356 2819 Planarity : 0.004 0.056 3213 Dihedral : 11.877 177.266 3229 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.87 % Allowed : 11.23 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.17), residues: 2286 helix: 1.19 (0.21), residues: 657 sheet: -0.01 (0.28), residues: 404 loop : -2.37 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.055 0.002 TYR C 295 PHE 0.010 0.001 PHE C 147 TRP 0.011 0.002 TRP H 311 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (18791) covalent geometry : angle 0.67858 / 0.33 (25693) hydrogen bonds : bond 0.03376 / 2.21 ( 716) hydrogen bonds : angle 4.53945 / 3.19 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5120.82 seconds wall clock time: 88 minutes 11.06 seconds (5291.06 seconds total)