Starting phenix.real_space_refine on Wed Nov 19 01:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6b46_7050/11_2025/6b46_7050.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b46_7050/11_2025/6b46_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_7050/11_2025/6b46_7050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b46_7050/11_2025/6b46_7050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b46_7050/11_2025/6b46_7050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b46_7050/11_2025/6b46_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-2.0-5881/lib/python3.9/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: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 19, 'rna3p': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.69, per 1000 atoms: 0.26 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: 1.60 Conformation dependent library (CDL) restraints added in 784.7 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: 1.79 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: 3.09 Time building geometry restraints manager: 2.17 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: 25152 2.54 - 5.09: 479 5.09 - 7.63: 47 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 - 30.12: 10763 30.12 - 60.23: 266 60.23 - 90.35: 77 90.35 - 120.47: 2 120.47 - 150.59: 2 Dihedral angle restraints: 11110 sinusoidal: 4819 harmonic: 6291 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 49.41 150.59 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 69.28 130.72 1 1.50e+01 4.44e-03 7.05e+01 dihedral pdb=" CA TRP C 270 " pdb=" C TRP C 270 " pdb=" N TYR C 271 " pdb=" CA TYR C 271 " ideal model delta harmonic sigma weight residual 180.00 148.86 31.14 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 11107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2718 0.115 - 0.231: 93 0.231 - 0.346: 7 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=" CB ILE D 267 " pdb=" CA ILE D 267 " pdb=" CG1 ILE D 267 " pdb=" CG2 ILE D 267 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' C M 1 " pdb=" C4' C M 1 " pdb=" O3' C M 1 " pdb=" C2' C M 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.77 0.27 2.00e-01 2.50e+01 1.80e+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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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= 0.261 Angle : 0.872 12.715 25693 Z= 0.490 Chirality : 0.054 0.577 2819 Planarity : 0.006 0.063 3213 Dihedral : 14.100 150.587 7178 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 covalent geometry : bond 0.00572 (18791) covalent geometry : angle 0.87236 (25693) hydrogen bonds : bond 0.20130 ( 716) hydrogen bonds : angle 8.16509 ( 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 : 0.689 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: 0.2092 time to fit residues: 77.5333 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 : 0.672 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3957 r_free = 0.3957 target = 0.150013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116861 restraints weight = 30770.331| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.56 r_work: 0.3351 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 18791 Z= 0.188 Angle : 0.633 7.829 25693 Z= 0.342 Chirality : 0.043 0.392 2819 Planarity : 0.005 0.064 3213 Dihedral : 15.804 149.026 3459 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.33 % Allowed : 5.43 % 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: -0.61 (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 0.007 0.001 ARG H 175 TYR 0.017 0.002 TYR E 305 PHE 0.021 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 covalent geometry : bond 0.00428 (18791) covalent geometry : angle 0.63304 (25693) hydrogen bonds : bond 0.04404 ( 716) hydrogen bonds : angle 5.44910 ( 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 193 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: C 83 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7436 (t0) REVERT: C 136 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7956 (mtm-85) REVERT: C 259 LYS cc_start: 0.8352 (tttt) cc_final: 0.7820 (tptt) REVERT: C 277 LEU cc_start: 0.6337 (mp) cc_final: 0.6108 (mp) REVERT: D 45 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7783 (mtm-85) REVERT: D 187 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7645 (mtmm) REVERT: F 228 SER cc_start: 0.8899 (p) cc_final: 0.8594 (m) REVERT: G 60 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8534 (pttt) REVERT: H 34 ASP cc_start: 0.7060 (m-30) cc_final: 0.6654 (t0) REVERT: H 212 GLU cc_start: 0.7681 (pp20) cc_final: 0.7314 (pp20) REVERT: H 262 ASN cc_start: 0.7561 (t0) cc_final: 0.7343 (t0) REVERT: H 321 GLU cc_start: 0.7001 (mp0) cc_final: 0.6312 (mt-10) REVERT: H 325 TYR cc_start: 0.7116 (t80) cc_final: 0.6716 (t80) REVERT: J 31 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7639 (mt-10) outliers start: 22 outliers final: 12 residues processed: 182 average time/residue: 0.1801 time to fit residues: 47.1530 Evaluate side-chains 157 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 170 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: 10.0000 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 225 optimal weight: 40.0000 chunk 43 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN D 164 HIS E 291 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113707 restraints weight = 31444.190| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.65 r_work: 0.3316 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18791 Z= 0.195 Angle : 0.613 6.746 25693 Z= 0.331 Chirality : 0.043 0.315 2819 Planarity : 0.005 0.062 3213 Dihedral : 15.751 150.135 3459 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.93 % Allowed : 7.12 % Favored : 90.95 % 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: -2.10 (0.17), residues: 2286 helix: 0.26 (0.20), residues: 659 sheet: -0.63 (0.27), residues: 401 loop : -2.74 (0.15), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 136 TYR 0.019 0.002 TYR E 305 PHE 0.025 0.002 PHE J 44 TRP 0.021 0.002 TRP E 311 HIS 0.009 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00446 (18791) covalent geometry : angle 0.61333 (25693) hydrogen bonds : bond 0.04090 ( 716) hydrogen bonds : angle 5.01305 ( 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 182 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7174 (mm-30) REVERT: C 259 LYS cc_start: 0.8405 (tttt) cc_final: 0.8113 (tttp) REVERT: C 277 LEU cc_start: 0.6370 (mp) cc_final: 0.6131 (mp) REVERT: D 45 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7798 (mtm-85) REVERT: F 32 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: G 60 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (pttt) REVERT: H 321 GLU cc_start: 0.7041 (mp0) cc_final: 0.6680 (mt-10) REVERT: I 25 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7848 (pttt) REVERT: I 39 VAL cc_start: 0.8334 (m) cc_final: 0.8079 (p) REVERT: J 52 SER cc_start: 0.8633 (p) cc_final: 0.8433 (p) outliers start: 32 outliers final: 20 residues processed: 169 average time/residue: 0.1709 time to fit residues: 41.8853 Evaluate side-chains 159 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 156 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 226 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS ** 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 = 0.146070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111963 restraints weight = 31560.085| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.58 r_work: 0.3265 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18791 Z= 0.256 Angle : 0.674 7.654 25693 Z= 0.361 Chirality : 0.045 0.349 2819 Planarity : 0.005 0.061 3213 Dihedral : 15.817 151.970 3459 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 2.23 % Allowed : 8.63 % Favored : 89.14 % 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: -1.97 (0.17), residues: 2286 helix: 0.45 (0.20), residues: 656 sheet: -0.58 (0.27), residues: 397 loop : -2.68 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 136 TYR 0.020 0.002 TYR E 305 PHE 0.012 0.002 PHE F 336 TRP 0.020 0.002 TRP E 311 HIS 0.008 0.002 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00593 (18791) covalent geometry : angle 0.67376 (25693) hydrogen bonds : bond 0.04368 ( 716) hydrogen bonds : angle 5.10597 ( 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 179 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8653 (mtp) cc_final: 0.8343 (mtt) REVERT: C 230 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7045 (mm-30) REVERT: C 259 LYS cc_start: 0.8395 (tttt) cc_final: 0.7900 (tptt) REVERT: D 45 ARG cc_start: 0.8034 (mtm110) cc_final: 0.7708 (mtm-85) REVERT: E 119 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7532 (mm) REVERT: F 32 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: G 80 ASP cc_start: 0.7939 (m-30) cc_final: 0.7545 (m-30) REVERT: H 224 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: H 262 ASN cc_start: 0.7636 (t0) cc_final: 0.7404 (t0) REVERT: H 321 GLU cc_start: 0.7013 (mp0) cc_final: 0.6730 (mt-10) REVERT: H 332 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4702 (tmt-80) REVERT: I 25 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7600 (pttt) REVERT: I 39 VAL cc_start: 0.8353 (m) cc_final: 0.8055 (p) REVERT: J 71 GLU cc_start: 0.7237 (tm-30) cc_final: 0.7019 (tm-30) outliers start: 37 outliers final: 23 residues processed: 165 average time/residue: 0.1577 time to fit residues: 38.7793 Evaluate side-chains 159 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 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 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 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 332 ARG Chi-restraints excluded: chain J residue 7 LEU 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: 3.9990 chunk 215 optimal weight: 40.0000 chunk 92 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 221 optimal weight: 40.0000 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN E 72 GLN F 241 GLN H 323 GLN I 49 GLN ** J 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115466 restraints weight = 31100.637| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.62 r_work: 0.3345 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18791 Z= 0.133 Angle : 0.542 7.512 25693 Z= 0.293 Chirality : 0.041 0.314 2819 Planarity : 0.004 0.056 3213 Dihedral : 15.560 152.039 3459 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.17 % Allowed : 10.32 % Favored : 87.51 % 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: -1.57 (0.17), residues: 2286 helix: 0.90 (0.21), residues: 657 sheet: -0.30 (0.28), residues: 408 loop : -2.55 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 136 TYR 0.015 0.002 TYR G 247 PHE 0.019 0.001 PHE J 44 TRP 0.012 0.001 TRP C 174 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd covalent geometry : bond 0.00298 (18791) covalent geometry : angle 0.54157 (25693) hydrogen bonds : bond 0.03302 ( 716) hydrogen bonds : angle 4.64949 ( 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 186 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8774 (mtp) cc_final: 0.8488 (mtt) REVERT: C 230 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7083 (mm-30) REVERT: D 45 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7783 (mtm-85) REVERT: E 119 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7603 (mm) REVERT: F 32 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: H 224 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: H 280 ILE cc_start: 0.6391 (pt) cc_final: 0.6110 (mt) REVERT: H 321 GLU cc_start: 0.7065 (mp0) cc_final: 0.6738 (mt-10) REVERT: H 323 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.5791 (mm-40) REVERT: H 332 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.4595 (tmt-80) REVERT: I 25 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7525 (pttt) REVERT: I 71 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8083 (tm-30) REVERT: J 71 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6973 (tm-30) REVERT: J 72 ILE cc_start: 0.8068 (mt) cc_final: 0.7648 (mt) outliers start: 36 outliers final: 24 residues processed: 175 average time/residue: 0.1771 time to fit residues: 44.9065 Evaluate side-chains 159 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 F residue 15 GLU 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 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 323 GLN Chi-restraints excluded: chain H residue 332 ARG Chi-restraints excluded: chain J residue 35 ASN Chi-restraints excluded: chain J residue 43 ASP 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: 9.9990 chunk 115 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 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 = 0.146184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111426 restraints weight = 31147.985| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.75 r_work: 0.3262 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18791 Z= 0.235 Angle : 0.638 8.614 25693 Z= 0.341 Chirality : 0.044 0.326 2819 Planarity : 0.005 0.055 3213 Dihedral : 15.714 153.095 3459 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 2.53 % Allowed : 11.35 % Favored : 86.12 % 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: -1.61 (0.17), residues: 2286 helix: 0.84 (0.21), residues: 653 sheet: -0.32 (0.28), residues: 390 loop : -2.52 (0.15), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 146 TYR 0.018 0.002 TYR H 325 PHE 0.012 0.002 PHE C 147 TRP 0.017 0.002 TRP E 311 HIS 0.013 0.002 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00543 (18791) covalent geometry : angle 0.63824 (25693) hydrogen bonds : bond 0.04117 ( 716) hydrogen bonds : angle 4.90879 ( 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 178 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8677 (mtp) cc_final: 0.8368 (mtt) REVERT: C 230 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6977 (mm-30) REVERT: C 259 LYS cc_start: 0.8377 (tttt) cc_final: 0.8071 (tttp) REVERT: D 45 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7663 (mtm-85) REVERT: E 119 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7511 (mm) REVERT: F 32 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: G 114 TYR cc_start: 0.7389 (t80) cc_final: 0.7059 (t80) REVERT: G 140 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7795 (t-90) REVERT: H 224 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6339 (tp30) REVERT: H 321 GLU cc_start: 0.6987 (mp0) cc_final: 0.6623 (mt-10) REVERT: I 25 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7476 (pttt) REVERT: J 71 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6843 (tm-30) outliers start: 42 outliers final: 33 residues processed: 167 average time/residue: 0.1681 time to fit residues: 41.1693 Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 277 LEU 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 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 250 ARG Chi-restraints excluded: chain D residue 266 THR 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 59 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 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 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: 30.0000 chunk 159 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114419 restraints weight = 31120.437| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.56 r_work: 0.3316 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18791 Z= 0.159 Angle : 0.564 7.207 25693 Z= 0.305 Chirality : 0.041 0.314 2819 Planarity : 0.004 0.051 3213 Dihedral : 15.599 152.965 3459 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.60 % Allowed : 11.83 % Favored : 85.58 % 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: -1.43 (0.17), residues: 2286 helix: 1.01 (0.21), residues: 655 sheet: -0.13 (0.28), residues: 396 loop : -2.47 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 152 TYR 0.015 0.002 TYR H 325 PHE 0.012 0.001 PHE J 44 TRP 0.012 0.002 TRP F 30 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd covalent geometry : bond 0.00363 (18791) covalent geometry : angle 0.56410 (25693) hydrogen bonds : bond 0.03491 ( 716) hydrogen bonds : angle 4.70112 ( 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 176 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8800 (mtp) cc_final: 0.8500 (mtt) REVERT: C 77 GLN cc_start: 0.0089 (OUTLIER) cc_final: -0.0552 (tp40) REVERT: C 230 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7059 (mm-30) REVERT: D 45 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7765 (mtm-85) REVERT: E 119 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7581 (mm) REVERT: F 32 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: G 140 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7794 (t-90) REVERT: H 224 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6348 (tp30) REVERT: H 321 GLU cc_start: 0.7019 (mp0) cc_final: 0.6713 (mt-10) REVERT: I 25 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7565 (pttt) REVERT: I 39 VAL cc_start: 0.8365 (m) cc_final: 0.8006 (p) REVERT: J 71 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6965 (tm-30) outliers start: 43 outliers final: 32 residues processed: 163 average time/residue: 0.1736 time to fit residues: 41.3845 Evaluate side-chains 164 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 124 THR 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 32 GLN Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 192 LEU 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 140 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 18 LEU 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 I residue 49 GLN Chi-restraints excluded: chain J residue 7 LEU 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: 7.9990 chunk 221 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 178 optimal weight: 0.0270 chunk 58 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 184 optimal weight: 0.0050 chunk 139 optimal weight: 9.9990 overall best weight: 5.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112339 restraints weight = 31210.631| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.72 r_work: 0.3294 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18791 Z= 0.208 Angle : 0.604 7.786 25693 Z= 0.324 Chirality : 0.043 0.319 2819 Planarity : 0.004 0.051 3213 Dihedral : 15.650 153.398 3459 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.84 % Allowed : 11.89 % Favored : 85.27 % 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: -1.50 (0.17), residues: 2286 helix: 0.98 (0.21), residues: 653 sheet: -0.26 (0.28), residues: 387 loop : -2.48 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 152 TYR 0.015 0.002 TYR H 114 PHE 0.012 0.002 PHE C 147 TRP 0.013 0.002 TRP F 30 HIS 0.005 0.002 HIS G 324 Details of bonding type rmsd covalent geometry : bond 0.00481 (18791) covalent geometry : angle 0.60410 (25693) hydrogen bonds : bond 0.03829 ( 716) hydrogen bonds : angle 4.79342 ( 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 181 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8802 (mtp) cc_final: 0.8514 (mtt) REVERT: C 230 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7139 (mm-30) REVERT: D 45 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7825 (mtm-85) REVERT: E 119 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7603 (mm) REVERT: F 32 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: G 140 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7838 (t-90) REVERT: H 224 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6359 (tp30) REVERT: H 321 GLU cc_start: 0.7059 (mp0) cc_final: 0.6734 (mt-10) REVERT: I 25 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7508 (pttt) REVERT: J 71 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 47 outliers final: 36 residues processed: 168 average time/residue: 0.1646 time to fit residues: 40.9541 Evaluate side-chains 174 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 270 TRP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 124 THR 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 76 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 127 ASN 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 192 LEU 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 99 VAL 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 332 ARG Chi-restraints excluded: chain J residue 7 LEU 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: 6.9990 chunk 223 optimal weight: 50.0000 chunk 28 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 210 optimal weight: 50.0000 chunk 182 optimal weight: 9.9990 chunk 217 optimal weight: 50.0000 chunk 161 optimal weight: 20.0000 chunk 220 optimal weight: 30.0000 chunk 224 optimal weight: 0.0770 chunk 123 optimal weight: 5.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN F 241 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112876 restraints weight = 31053.598| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.58 r_work: 0.3307 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18791 Z= 0.190 Angle : 0.591 7.825 25693 Z= 0.317 Chirality : 0.042 0.315 2819 Planarity : 0.004 0.050 3213 Dihedral : 15.629 153.550 3459 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.66 % Allowed : 12.19 % Favored : 85.15 % 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: -1.46 (0.17), residues: 2286 helix: 1.03 (0.21), residues: 654 sheet: -0.22 (0.28), residues: 386 loop : -2.47 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 146 TYR 0.015 0.002 TYR H 114 PHE 0.012 0.001 PHE J 44 TRP 0.013 0.002 TRP F 30 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd covalent geometry : bond 0.00436 (18791) covalent geometry : angle 0.59086 (25693) hydrogen bonds : bond 0.03701 ( 716) hydrogen bonds : angle 4.75019 ( 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 174 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8796 (mtp) cc_final: 0.8507 (mtt) REVERT: C 230 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 45 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7836 (mtm-85) REVERT: E 119 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7592 (mm) REVERT: F 32 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: G 140 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7811 (t-90) REVERT: H 224 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6345 (tp30) REVERT: H 321 GLU cc_start: 0.7032 (mp0) cc_final: 0.6702 (mt-10) REVERT: I 25 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7457 (pttt) REVERT: J 71 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6950 (tm-30) outliers start: 44 outliers final: 36 residues processed: 160 average time/residue: 0.1683 time to fit residues: 39.7167 Evaluate side-chains 165 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 124 THR 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 162 ILE Chi-restraints excluded: chain F residue 192 LEU 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 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 99 VAL 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 332 ARG Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain J residue 7 LEU 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: 10.0000 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112926 restraints weight = 31217.833| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.49 r_work: 0.3300 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18791 Z= 0.182 Angle : 0.589 8.309 25693 Z= 0.316 Chirality : 0.042 0.313 2819 Planarity : 0.004 0.049 3213 Dihedral : 15.606 153.599 3459 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.72 % Allowed : 12.37 % Favored : 84.91 % 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: -1.44 (0.17), residues: 2286 helix: 1.07 (0.21), residues: 653 sheet: -0.22 (0.28), residues: 388 loop : -2.46 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 152 TYR 0.018 0.002 TYR C 295 PHE 0.011 0.001 PHE C 147 TRP 0.013 0.002 TRP F 30 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd covalent geometry : bond 0.00418 (18791) covalent geometry : angle 0.58922 (25693) hydrogen bonds : bond 0.03649 ( 716) hydrogen bonds : angle 4.71951 ( 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 173 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 MET cc_start: 0.8817 (mtp) cc_final: 0.8528 (mtt) REVERT: C 77 GLN cc_start: 0.0058 (OUTLIER) cc_final: -0.0625 (tp40) REVERT: C 230 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 45 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7862 (mtm-85) REVERT: E 119 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7615 (mm) REVERT: F 32 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8200 (mp10) REVERT: G 140 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7806 (t-90) REVERT: H 45 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7365 (mtp-110) REVERT: H 224 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: H 321 GLU cc_start: 0.7024 (mp0) cc_final: 0.6708 (mt-10) REVERT: I 25 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7428 (pttt) REVERT: J 71 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6954 (tm-30) outliers start: 45 outliers final: 34 residues processed: 158 average time/residue: 0.1585 time to fit residues: 37.2538 Evaluate side-chains 165 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 124 THR 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 76 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 127 ASN 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 192 LEU 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 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 45 ARG 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 199 ILE 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 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: 7.9990 chunk 97 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 191 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111299 restraints weight = 31231.680| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.60 r_work: 0.3283 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18791 Z= 0.240 Angle : 0.645 8.598 25693 Z= 0.344 Chirality : 0.044 0.321 2819 Planarity : 0.005 0.051 3213 Dihedral : 15.702 153.908 3459 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.72 % Allowed : 12.25 % Favored : 85.03 % 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: 0.90 (0.21), residues: 653 sheet: -0.10 (0.27), residues: 403 loop : -2.53 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 152 TYR 0.015 0.002 TYR H 114 PHE 0.013 0.002 PHE C 147 TRP 0.017 0.002 TRP C 270 HIS 0.006 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00558 (18791) covalent geometry : angle 0.64461 (25693) hydrogen bonds : bond 0.04075 ( 716) hydrogen bonds : angle 4.87437 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5159.08 seconds wall clock time: 88 minutes 46.25 seconds (5326.25 seconds total)