Starting phenix.real_space_refine on Sat Sep 12 11:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlo_6729/09_2026/5xlo_6729.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 38 5.49 5 S 18 5.16 5 C 9455 2.51 5 N 2690 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15413 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2004 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 14, 'ASP:plan': 1, 'TRP:plan': 4, 'TYR:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "F" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2273 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 12, 'TRANS': 313} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 15, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 5, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 195 Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 809 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 17, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 29, 'rna3p': 8} Chain: "N" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 615 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 620 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Time building chain proxies: 3.53, per 1000 atoms: 0.23 Number of scatterers: 15413 At special positions: 0 Unit cell: (126.1, 143, 113.1, 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 38 15.00 O 3212 8.00 N 2690 7.00 C 9455 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: 1.28 Conformation dependent library (CDL) restraints added in 675.2 milliseconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3830 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 30.1% alpha, 7.9% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 removed outlier: 4.039A pdb=" N GLN B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 78 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU B 191 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.682A pdb=" N VAL B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU B 316 " --> pdb=" O LEU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 316' Processing helix chain 'B' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 4.166A pdb=" N VAL C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU C 191 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 275 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.231A pdb=" N GLN C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 316 removed outlier: 3.529A pdb=" N GLU C 316 " --> pdb=" O LEU C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 316' Processing helix chain 'C' and resid 317 through 325 removed outlier: 5.201A pdb=" N GLN C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 83 removed outlier: 4.420A pdb=" N THR D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 141 through 151 Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.719A pdb=" N GLU D 191 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 275 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU D 316 " --> pdb=" O LEU D 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 316' Processing helix chain 'D' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU D 338 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 340 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 81 removed outlier: 3.938A pdb=" N VAL E 79 " --> pdb=" O ASN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 138 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.720A pdb=" N GLU E 191 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 214 removed outlier: 3.683A pdb=" N VAL E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 275 Proline residue: E 272 - end of helix Processing helix chain 'E' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 removed outlier: 3.527A pdb=" N GLU E 316 " --> pdb=" O LEU E 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY E 337 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 83 removed outlier: 4.524A pdb=" N VAL F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN F 83 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 138 Processing helix chain 'F' and resid 141 through 151 Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.720A pdb=" N GLU F 191 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 214 removed outlier: 3.682A pdb=" N VAL F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 275 Proline residue: F 272 - end of helix Processing helix chain 'F' and resid 293 through 297 removed outlier: 4.232A pdb=" N GLN F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 316 removed outlier: 3.528A pdb=" N GLU F 316 " --> pdb=" O LEU F 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 316' Processing helix chain 'F' and resid 317 through 325 removed outlier: 5.200A pdb=" N GLN F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 340 removed outlier: 4.602A pdb=" N GLY F 337 " --> pdb=" O GLY F 333 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 56 removed outlier: 3.799A pdb=" N SER N 52 " --> pdb=" O GLU N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 74 removed outlier: 3.867A pdb=" N ILE N 65 " --> pdb=" O GLY N 61 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG N 74 " --> pdb=" O ASN N 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 56 removed outlier: 3.800A pdb=" N SER M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 74 removed outlier: 3.867A pdb=" N ILE M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG M 74 " --> pdb=" O ASN M 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA A 23 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 108 Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA B 23 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 60 removed outlier: 8.199A pdb=" N ALA B 252 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA B 88 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA B 254 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 108 Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 23 removed outlier: 4.055A pdb=" N ALA C 23 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 108 Processing sheet with id=AA9, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.057A pdb=" N ALA D 23 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 58 Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 108 Processing sheet with id=AB3, first strand: chain 'E' and resid 22 through 23 removed outlier: 4.055A pdb=" N ALA E 23 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59 Processing sheet with id=AB5, first strand: chain 'E' and resid 104 through 108 Processing sheet with id=AB6, first strand: chain 'F' and resid 22 through 23 removed outlier: 4.056A pdb=" N ALA F 23 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 57 through 58 Processing sheet with id=AB8, first strand: chain 'F' and resid 104 through 108 Processing sheet with id=AB9, first strand: chain 'N' and resid 15 through 16 Processing sheet with id=AC1, first strand: chain 'N' and resid 19 through 21 Processing sheet with id=AC2, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 21 415 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.68 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: 4069 1.33 - 1.45: 2822 1.45 - 1.57: 8714 1.57 - 1.69: 75 1.69 - 1.81: 30 Bond restraints: 15710 Sorted by residual: bond pdb=" C2 C K 12 " pdb=" N3 C K 12 " ideal model delta sigma weight residual 1.353 1.324 0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" N9 A K 28 " pdb=" C4 A K 28 " ideal model delta sigma weight residual 1.374 1.394 -0.020 6.00e-03 2.78e+04 1.11e+01 bond pdb=" N1 U K 31 " pdb=" C2 U K 31 " ideal model delta sigma weight residual 1.381 1.411 -0.030 9.00e-03 1.23e+04 1.08e+01 bond pdb=" N1 C K 20 " pdb=" C6 C K 20 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.04e+01 bond pdb=" N1 C K 29 " pdb=" C2 C K 29 " ideal model delta sigma weight residual 1.397 1.429 -0.032 1.00e-02 1.00e+04 1.01e+01 ... (remaining 15705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 20649 2.88 - 5.75: 794 5.75 - 8.63: 121 8.63 - 11.50: 51 11.50 - 14.38: 12 Bond angle restraints: 21627 Sorted by residual: angle pdb=" N1 C K 29 " pdb=" C2 C K 29 " pdb=" O2 C K 29 " ideal model delta sigma weight residual 118.90 126.95 -8.05 6.00e-01 2.78e+00 1.80e+02 angle pdb=" C1' C K 29 " pdb=" N1 C K 29 " pdb=" C2 C K 29 " ideal model delta sigma weight residual 118.80 133.18 -14.38 1.10e+00 8.26e-01 1.71e+02 angle pdb=" N1 U K 31 " pdb=" C2 U K 31 " pdb=" O2 U K 31 " ideal model delta sigma weight residual 122.80 131.03 -8.23 7.00e-01 2.04e+00 1.38e+02 angle pdb=" C1' U K 31 " pdb=" N1 U K 31 " pdb=" C2 U K 31 " ideal model delta sigma weight residual 117.70 131.39 -13.69 1.20e+00 6.94e-01 1.30e+02 angle pdb=" O2 C K 29 " pdb=" C2 C K 29 " pdb=" N3 C K 29 " ideal model delta sigma weight residual 121.90 114.08 7.82 7.00e-01 2.04e+00 1.25e+02 ... (remaining 21622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.17: 9238 34.17 - 68.34: 167 68.34 - 102.51: 32 102.51 - 136.67: 3 136.67 - 170.84: 5 Dihedral angle restraints: 9445 sinusoidal: 3513 harmonic: 5932 Sorted by residual: dihedral pdb=" CA ALA M 10 " pdb=" C ALA M 10 " pdb=" N HIS M 11 " pdb=" CA HIS M 11 " ideal model delta harmonic sigma weight residual 180.00 45.61 134.39 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA ALA N 10 " pdb=" C ALA N 10 " pdb=" N HIS N 11 " pdb=" CA HIS N 11 " ideal model delta harmonic sigma weight residual 180.00 45.65 134.35 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA HIS M 11 " pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta harmonic sigma weight residual -180.00 -124.51 -55.49 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 9442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2223 0.086 - 0.172: 353 0.172 - 0.258: 29 0.258 - 0.344: 8 0.344 - 0.430: 2 Chirality restraints: 2615 Sorted by residual: chirality pdb=" C3' A K 4 " pdb=" C4' A K 4 " pdb=" O3' A K 4 " pdb=" C2' A K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C3' G K 9 " pdb=" C4' G K 9 " pdb=" O3' G K 9 " pdb=" C2' G K 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' A K 28 " pdb=" C4' A K 28 " pdb=" O3' A K 28 " pdb=" C2' A K 28 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 2612 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS N 11 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C HIS N 11 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS N 11 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU N 12 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS M 11 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C HIS M 11 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS M 11 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU M 12 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 317 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO F 318 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO F 318 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 318 " -0.038 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 268 2.62 - 3.19: 13712 3.19 - 3.76: 22598 3.76 - 4.33: 31434 4.33 - 4.90: 49707 Nonbonded interactions: 117719 Sorted by model distance: nonbonded pdb=" NZ LYS E 244 " pdb=" O SER F 248 " model vdw 2.050 3.120 nonbonded pdb=" N LYS C 60 " pdb=" OP2 U K 25 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASP F 80 " pdb=" OH TYR N 6 " model vdw 2.180 3.040 nonbonded pdb=" OG1 THR C 90 " pdb=" O ALA C 254 " model vdw 2.230 3.040 nonbonded pdb=" NZ LYS A 293 " pdb=" OP1 C K 30 " model vdw 2.233 3.120 ... (remaining 117714 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 'A' selection = (chain 'B' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'C' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'D' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'E' and (resid 15 through 53 or resid 93 through 340)) selection = (chain 'F' and (resid 15 through 53 or resid 93 through 340)) } ncs_group { reference = (chain 'M' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 78)) selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 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 : 0.009 0.106 15710 Z= 0.451 Angle : 1.375 14.376 21627 Z= 0.812 Chirality : 0.065 0.430 2615 Planarity : 0.008 0.065 2759 Dihedral : 15.312 170.842 5615 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.78 % Allowed : 17.27 % Favored : 81.95 % Rotamer: Outliers : 0.29 % Allowed : 2.87 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -6.02 (0.12), residues: 2055 helix: -4.14 (0.10), residues: 442 sheet: -3.84 (0.21), residues: 320 loop : -4.22 (0.12), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 172 TYR 0.020 0.002 TYR M 20 PHE 0.027 0.004 PHE E 336 TRP 0.021 0.004 TRP F 270 HIS 0.012 0.003 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.45 (15710) covalent geometry : angle 1.37488 / 0.81 (21627) hydrogen bonds : bond 0.19711 / 14.02 ( 415) hydrogen bonds : angle 13.61624 / 9.52 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 452 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.6661 (mp) cc_final: 0.6405 (tt) REVERT: A 270 TRP cc_start: 0.6527 (t-100) cc_final: 0.6031 (t-100) REVERT: B 24 LEU cc_start: 0.8048 (mp) cc_final: 0.7615 (mp) REVERT: B 214 VAL cc_start: 0.7705 (t) cc_final: 0.7383 (p) REVERT: B 239 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7433 (mmtt) REVERT: B 332 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7656 (mtt180) REVERT: C 46 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6321 (tt0) REVERT: C 58 LYS cc_start: 0.7297 (mttt) cc_final: 0.6655 (mttt) REVERT: C 91 LEU cc_start: 0.7295 (mt) cc_final: 0.6498 (mt) REVERT: D 58 LYS cc_start: 0.7634 (mttt) cc_final: 0.7418 (mttt) REVERT: D 91 LEU cc_start: 0.7289 (mt) cc_final: 0.7039 (mt) REVERT: D 127 ASN cc_start: 0.8169 (m-40) cc_final: 0.7900 (m-40) REVERT: D 131 PHE cc_start: 0.7596 (m-80) cc_final: 0.7335 (m-80) REVERT: D 234 ASP cc_start: 0.6790 (m-30) cc_final: 0.6394 (t0) REVERT: D 267 ILE cc_start: 0.8047 (mt) cc_final: 0.7810 (mt) REVERT: E 25 MET cc_start: 0.4921 (mmm) cc_final: 0.4521 (mmm) REVERT: E 125 TYR cc_start: 0.6944 (t80) cc_final: 0.6288 (t80) REVERT: E 131 PHE cc_start: 0.6337 (m-80) cc_final: 0.6091 (m-80) REVERT: E 275 ASP cc_start: 0.6848 (t70) cc_final: 0.6538 (t0) REVERT: F 116 ASP cc_start: 0.8191 (m-30) cc_final: 0.7223 (p0) REVERT: F 144 ASN cc_start: 0.5234 (m-40) cc_final: 0.4881 (m110) REVERT: F 163 ASN cc_start: 0.7872 (m-40) cc_final: 0.7504 (m-40) REVERT: F 172 ARG cc_start: 0.6061 (mtt-85) cc_final: 0.5684 (mtt90) REVERT: F 308 LEU cc_start: 0.5927 (mt) cc_final: 0.5429 (tp) REVERT: N 50 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6242 (tm) REVERT: M 29 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6909 (ptm160) outliers start: 4 outliers final: 0 residues processed: 454 average time/residue: 0.1320 time to fit residues: 86.3157 Evaluate side-chains 346 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN A 229 GLN A 256 HIS B 83 ASN B 141 ASN B 144 ASN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 324 HIS E 72 GLN E 110 ASN E 256 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN F 72 GLN F 110 ASN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN M 49 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.233420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.212111 restraints weight = 20295.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.212525 restraints weight = 22344.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.213689 restraints weight = 18147.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.213862 restraints weight = 14534.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.214182 restraints weight = 12551.420| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15710 Z= 0.191 Angle : 0.939 15.258 21627 Z= 0.483 Chirality : 0.048 0.435 2615 Planarity : 0.007 0.108 2759 Dihedral : 17.936 171.219 2770 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.73 % Allowed : 14.11 % Favored : 85.16 % Rotamer: Outliers : 4.35 % Allowed : 11.42 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -5.24 (0.14), residues: 2055 helix: -2.91 (0.18), residues: 444 sheet: -3.56 (0.23), residues: 290 loop : -3.91 (0.13), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 94 TYR 0.015 0.002 TYR N 20 PHE 0.020 0.002 PHE F 176 TRP 0.023 0.002 TRP B 270 HIS 0.009 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (15710) covalent geometry : angle 0.93871 / 0.48 (21627) hydrogen bonds : bond 0.05107 / 3.55 ( 415) hydrogen bonds : angle 8.88917 / 6.19 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5771 (mt0) cc_final: 0.5508 (mt0) REVERT: A 131 PHE cc_start: 0.6951 (m-80) cc_final: 0.6189 (m-80) REVERT: A 270 TRP cc_start: 0.6248 (t-100) cc_final: 0.5837 (t-100) REVERT: A 280 ILE cc_start: 0.5196 (mt) cc_final: 0.4977 (mt) REVERT: A 338 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7011 (mt-10) REVERT: B 169 GLU cc_start: 0.5682 (tt0) cc_final: 0.5210 (pt0) REVERT: B 314 ARG cc_start: 0.7550 (mmm160) cc_final: 0.6884 (tpt90) REVERT: C 42 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8065 (t) REVERT: C 58 LYS cc_start: 0.7227 (mttt) cc_final: 0.6718 (mttt) REVERT: C 91 LEU cc_start: 0.7416 (mt) cc_final: 0.7144 (mt) REVERT: C 336 PHE cc_start: 0.6719 (m-80) cc_final: 0.5942 (m-80) REVERT: D 234 ASP cc_start: 0.6723 (m-30) cc_final: 0.6518 (t0) REVERT: E 42 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7350 (t) REVERT: E 125 TYR cc_start: 0.7221 (t80) cc_final: 0.6737 (t80) REVERT: F 308 LEU cc_start: 0.6277 (mt) cc_final: 0.5767 (tp) outliers start: 59 outliers final: 29 residues processed: 396 average time/residue: 0.1328 time to fit residues: 76.0433 Evaluate side-chains 356 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 325 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN A 329 ASN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 GLN E 324 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 141 ASN F 256 HIS F 310 ASN M 49 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.211881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185881 restraints weight = 20235.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.186100 restraints weight = 22517.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.187877 restraints weight = 17035.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.189346 restraints weight = 12299.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.189535 restraints weight = 10620.436| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 15710 Z= 0.331 Angle : 1.083 16.611 21627 Z= 0.554 Chirality : 0.054 0.548 2615 Planarity : 0.008 0.099 2759 Dihedral : 17.980 171.988 2770 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.68 % Allowed : 19.22 % Favored : 80.10 % Rotamer: Outliers : 5.75 % Allowed : 12.01 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -5.34 (0.14), residues: 2055 helix: -2.62 (0.20), residues: 433 sheet: -3.88 (0.21), residues: 346 loop : -4.01 (0.13), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 314 TYR 0.025 0.003 TYR D 125 PHE 0.029 0.003 PHE E 131 TRP 0.044 0.004 TRP B 270 HIS 0.014 0.002 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.33 (15710) covalent geometry : angle 1.08270 / 0.55 (21627) hydrogen bonds : bond 0.05044 / 3.44 ( 415) hydrogen bonds : angle 8.32331 / 5.72 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6340 (mt0) cc_final: 0.6013 (mt0) REVERT: A 218 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.5456 (ttp-170) REVERT: A 270 TRP cc_start: 0.6600 (t-100) cc_final: 0.5758 (t-100) REVERT: A 280 ILE cc_start: 0.5436 (mt) cc_final: 0.5119 (mt) REVERT: B 169 GLU cc_start: 0.5832 (tt0) cc_final: 0.5175 (pt0) REVERT: B 197 GLU cc_start: 0.6946 (pp20) cc_final: 0.6734 (pm20) REVERT: B 239 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7608 (mttt) REVERT: B 300 GLN cc_start: 0.6755 (mp10) cc_final: 0.6530 (mm-40) REVERT: B 318 PRO cc_start: 0.6123 (Cg_endo) cc_final: 0.5845 (Cg_exo) REVERT: B 331 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6641 (tp) REVERT: B 332 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7516 (mtt180) REVERT: B 336 PHE cc_start: 0.6901 (m-80) cc_final: 0.5818 (m-80) REVERT: C 58 LYS cc_start: 0.7408 (mttt) cc_final: 0.6690 (mttt) REVERT: C 336 PHE cc_start: 0.6844 (m-80) cc_final: 0.6396 (m-80) REVERT: D 218 ARG cc_start: 0.5376 (tmm-80) cc_final: 0.4687 (tmm-80) REVERT: E 42 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (t) REVERT: E 125 TYR cc_start: 0.7881 (t80) cc_final: 0.7376 (t80) REVERT: E 131 PHE cc_start: 0.6332 (m-80) cc_final: 0.5888 (m-80) REVERT: E 176 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.5584 (m-80) REVERT: F 46 GLU cc_start: 0.7397 (tt0) cc_final: 0.6836 (tt0) REVERT: F 144 ASN cc_start: 0.5916 (m-40) cc_final: 0.5545 (m-40) REVERT: F 163 ASN cc_start: 0.8127 (m-40) cc_final: 0.7756 (m110) REVERT: F 234 ASP cc_start: 0.7275 (t0) cc_final: 0.6971 (t0) REVERT: F 308 LEU cc_start: 0.6669 (mt) cc_final: 0.5969 (tp) REVERT: N 47 THR cc_start: 0.8067 (m) cc_final: 0.7802 (t) REVERT: M 29 ARG cc_start: 0.7119 (ptm160) cc_final: 0.6794 (ptp-110) outliers start: 78 outliers final: 45 residues processed: 404 average time/residue: 0.1362 time to fit residues: 79.5364 Evaluate side-chains 385 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 336 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 53 TRP Chi-restraints excluded: chain M residue 73 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 166 optimal weight: 0.0870 chunk 148 optimal weight: 0.0070 chunk 155 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 329 ASN B 163 ASN B 256 HIS B 310 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 141 ASN F 144 ASN M 49 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.221663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198399 restraints weight = 19265.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.198725 restraints weight = 21038.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.200779 restraints weight = 16074.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.200890 restraints weight = 11645.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.201395 restraints weight = 11026.190| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 15710 Z= 0.157 Angle : 0.864 12.573 21627 Z= 0.440 Chirality : 0.046 0.367 2615 Planarity : 0.006 0.077 2759 Dihedral : 17.502 174.063 2770 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.31 % Favored : 87.15 % Rotamer: Outliers : 5.01 % Allowed : 14.96 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.78 (0.15), residues: 2055 helix: -1.73 (0.23), residues: 420 sheet: -3.65 (0.22), residues: 300 loop : -3.80 (0.14), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 172 TYR 0.019 0.002 TYR N 20 PHE 0.020 0.002 PHE E 131 TRP 0.044 0.002 TRP C 270 HIS 0.009 0.002 HIS M 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (15710) covalent geometry : angle 0.86354 / 0.44 (21627) hydrogen bonds : bond 0.03926 / 2.66 ( 415) hydrogen bonds : angle 7.54801 / 5.18 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 346 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ASN cc_start: 0.4192 (m-40) cc_final: 0.3576 (m-40) REVERT: A 270 TRP cc_start: 0.6122 (t-100) cc_final: 0.5326 (t-100) REVERT: A 332 ARG cc_start: 0.7868 (mtp85) cc_final: 0.6179 (ttp80) REVERT: B 169 GLU cc_start: 0.5875 (tt0) cc_final: 0.5332 (pt0) REVERT: B 239 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7555 (mttt) REVERT: B 300 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6302 (mm-40) REVERT: B 318 PRO cc_start: 0.6092 (Cg_endo) cc_final: 0.5726 (Cg_exo) REVERT: B 331 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6452 (tp) REVERT: B 332 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7994 (mtt180) REVERT: C 34 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.6801 (p0) REVERT: C 58 LYS cc_start: 0.6919 (mttt) cc_final: 0.6506 (mttt) REVERT: C 208 HIS cc_start: 0.7066 (t-170) cc_final: 0.6710 (t-170) REVERT: D 218 ARG cc_start: 0.4866 (tmm-80) cc_final: 0.4289 (tmm-80) REVERT: E 42 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7542 (t) REVERT: E 125 TYR cc_start: 0.7559 (t80) cc_final: 0.6911 (t80) REVERT: E 131 PHE cc_start: 0.5685 (m-80) cc_final: 0.5310 (m-80) REVERT: F 46 GLU cc_start: 0.6996 (tt0) cc_final: 0.6689 (tt0) REVERT: F 116 ASP cc_start: 0.7553 (p0) cc_final: 0.7021 (m-30) REVERT: F 144 ASN cc_start: 0.5255 (m110) cc_final: 0.4877 (m-40) REVERT: F 163 ASN cc_start: 0.7950 (m-40) cc_final: 0.7561 (m110) REVERT: F 234 ASP cc_start: 0.7178 (t0) cc_final: 0.6858 (t0) REVERT: F 308 LEU cc_start: 0.6149 (mt) cc_final: 0.5590 (tp) REVERT: F 336 PHE cc_start: 0.6311 (m-80) cc_final: 0.6029 (m-80) REVERT: N 53 TRP cc_start: 0.6651 (p-90) cc_final: 0.6434 (p-90) outliers start: 68 outliers final: 35 residues processed: 382 average time/residue: 0.1291 time to fit residues: 72.0159 Evaluate side-chains 364 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 300 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 140 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 323 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN D 262 ASN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN M 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.206374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178587 restraints weight = 20025.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179807 restraints weight = 18638.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.181597 restraints weight = 13961.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181920 restraints weight = 10470.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.182117 restraints weight = 10108.587| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.148 15710 Z= 0.406 Angle : 1.135 17.902 21627 Z= 0.577 Chirality : 0.056 0.585 2615 Planarity : 0.008 0.094 2759 Dihedral : 17.837 171.473 2768 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.83 % Allowed : 20.92 % Favored : 78.25 % Rotamer: Outliers : 6.12 % Allowed : 15.48 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % 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: -5.18 (0.15), residues: 2055 helix: -2.41 (0.20), residues: 465 sheet: -3.73 (0.21), residues: 351 loop : -3.96 (0.14), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 94 TYR 0.023 0.003 TYR B 125 PHE 0.030 0.004 PHE B 147 TRP 0.040 0.004 TRP C 270 HIS 0.018 0.003 HIS M 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.41 (15710) covalent geometry : angle 1.13540 / 0.58 (21627) hydrogen bonds : bond 0.04813 / 3.28 ( 415) hydrogen bonds : angle 7.83946 / 5.37 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 349 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5904 (mt0) cc_final: 0.5696 (tt0) REVERT: A 144 ASN cc_start: 0.4519 (m-40) cc_final: 0.3775 (m-40) REVERT: A 270 TRP cc_start: 0.6594 (t-100) cc_final: 0.5643 (t-100) REVERT: A 305 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6369 (m-10) REVERT: A 332 ARG cc_start: 0.7908 (mtp85) cc_final: 0.5762 (ttp80) REVERT: B 169 GLU cc_start: 0.5998 (tt0) cc_final: 0.5460 (pt0) REVERT: B 197 GLU cc_start: 0.7193 (pm20) cc_final: 0.6961 (pm20) REVERT: B 239 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7740 (mttt) REVERT: B 336 PHE cc_start: 0.7099 (m-80) cc_final: 0.6162 (m-80) REVERT: C 58 LYS cc_start: 0.7278 (mttt) cc_final: 0.6676 (mttt) REVERT: C 100 LEU cc_start: 0.6717 (mt) cc_final: 0.6456 (mt) REVERT: C 336 PHE cc_start: 0.6773 (m-80) cc_final: 0.6447 (m-80) REVERT: D 270 TRP cc_start: 0.7075 (t-100) cc_final: 0.6762 (t-100) REVERT: E 42 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7819 (t) REVERT: E 125 TYR cc_start: 0.8148 (t80) cc_final: 0.7673 (t80) REVERT: E 131 PHE cc_start: 0.6362 (m-80) cc_final: 0.5754 (m-80) REVERT: E 176 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: F 46 GLU cc_start: 0.7336 (tt0) cc_final: 0.6946 (tt0) REVERT: F 144 ASN cc_start: 0.6092 (m110) cc_final: 0.5583 (m110) REVERT: F 172 ARG cc_start: 0.5327 (OUTLIER) cc_final: 0.4815 (mtt90) REVERT: F 293 LYS cc_start: 0.8308 (tptt) cc_final: 0.7752 (tptt) REVERT: F 308 LEU cc_start: 0.6346 (mt) cc_final: 0.5879 (tp) REVERT: N 71 GLU cc_start: 0.8192 (tp30) cc_final: 0.7958 (tp30) REVERT: M 71 GLU cc_start: 0.8000 (mm-30) cc_final: 0.6973 (mt-10) outliers start: 83 outliers final: 58 residues processed: 392 average time/residue: 0.1415 time to fit residues: 79.8845 Evaluate side-chains 387 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 325 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 269 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 15 MET Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 323 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 110 ASN M 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.218136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.196059 restraints weight = 19639.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.195941 restraints weight = 23793.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.197453 restraints weight = 17623.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.197823 restraints weight = 13235.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.198202 restraints weight = 11467.106| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15710 Z= 0.164 Angle : 0.878 11.246 21627 Z= 0.447 Chirality : 0.047 0.391 2615 Planarity : 0.006 0.078 2759 Dihedral : 17.389 175.655 2768 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.80 % Favored : 86.67 % Rotamer: Outliers : 4.94 % Allowed : 18.13 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.62 (0.16), residues: 2055 helix: -1.74 (0.23), residues: 453 sheet: -3.54 (0.23), residues: 300 loop : -3.67 (0.14), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 94 TYR 0.018 0.002 TYR N 20 PHE 0.017 0.002 PHE F 176 TRP 0.044 0.003 TRP C 270 HIS 0.011 0.002 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15710) covalent geometry : angle 0.87817 / 0.45 (21627) hydrogen bonds : bond 0.03821 / 2.65 ( 415) hydrogen bonds : angle 7.19591 / 4.93 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5626 (mt0) cc_final: 0.5408 (tt0) REVERT: A 144 ASN cc_start: 0.4021 (m-40) cc_final: 0.3315 (m-40) REVERT: A 314 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.4516 (ttp80) REVERT: A 332 ARG cc_start: 0.7977 (mtp85) cc_final: 0.6257 (ttp80) REVERT: B 148 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6480 (tp) REVERT: B 169 GLU cc_start: 0.5951 (tt0) cc_final: 0.5480 (pt0) REVERT: B 197 GLU cc_start: 0.6949 (pm20) cc_final: 0.6639 (pm20) REVERT: B 239 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7847 (mttt) REVERT: B 314 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7544 (mmm160) REVERT: B 331 ILE cc_start: 0.6624 (OUTLIER) cc_final: 0.6366 (tp) REVERT: C 58 LYS cc_start: 0.6900 (mttt) cc_final: 0.6590 (mttt) REVERT: D 179 LEU cc_start: 0.7846 (mt) cc_final: 0.7488 (tp) REVERT: D 218 ARG cc_start: 0.5180 (tmm-80) cc_final: 0.4631 (tmm-80) REVERT: E 42 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7495 (t) REVERT: E 125 TYR cc_start: 0.7828 (t80) cc_final: 0.7369 (t80) REVERT: E 131 PHE cc_start: 0.5654 (m-80) cc_final: 0.5336 (m-80) REVERT: F 144 ASN cc_start: 0.5398 (m110) cc_final: 0.5060 (m110) REVERT: N 51 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7088 (mm-30) REVERT: N 71 GLU cc_start: 0.7999 (tp30) cc_final: 0.7436 (tp30) REVERT: M 71 GLU cc_start: 0.7980 (mm-30) cc_final: 0.6921 (mt-10) outliers start: 67 outliers final: 43 residues processed: 361 average time/residue: 0.1339 time to fit residues: 70.3970 Evaluate side-chains 358 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 59 optimal weight: 0.0670 chunk 194 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 110 ASN N 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.206866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179474 restraints weight = 19594.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179794 restraints weight = 17303.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.181507 restraints weight = 14283.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182589 restraints weight = 10747.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182796 restraints weight = 9570.786| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 15710 Z= 0.323 Angle : 1.034 16.480 21627 Z= 0.524 Chirality : 0.053 0.526 2615 Planarity : 0.007 0.085 2759 Dihedral : 17.616 172.342 2768 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.63 % Allowed : 20.92 % Favored : 78.44 % Rotamer: Outliers : 6.85 % Allowed : 17.32 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.70 % 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: -4.87 (0.15), residues: 2055 helix: -2.04 (0.22), residues: 455 sheet: -3.64 (0.24), residues: 290 loop : -3.81 (0.14), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 314 TYR 0.026 0.002 TYR A 305 PHE 0.028 0.003 PHE B 147 TRP 0.045 0.003 TRP C 270 HIS 0.011 0.003 HIS M 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.32 (15710) covalent geometry : angle 1.03431 / 0.52 (21627) hydrogen bonds : bond 0.04254 / 2.92 ( 415) hydrogen bonds : angle 7.48070 / 5.13 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 325 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6073 (mt0) cc_final: 0.5805 (tt0) REVERT: A 144 ASN cc_start: 0.4352 (m-40) cc_final: 0.3603 (m-40) REVERT: A 305 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6317 (m-10) REVERT: A 314 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6136 (mtp85) REVERT: A 332 ARG cc_start: 0.7916 (mtp85) cc_final: 0.5862 (ttp80) REVERT: B 148 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6744 (tp) REVERT: B 169 GLU cc_start: 0.5809 (tt0) cc_final: 0.5377 (pt0) REVERT: B 197 GLU cc_start: 0.7119 (pm20) cc_final: 0.6906 (pm20) REVERT: B 239 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7791 (mttt) REVERT: B 331 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6561 (tp) REVERT: C 25 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5335 (mmm) REVERT: C 58 LYS cc_start: 0.7125 (mttt) cc_final: 0.6625 (mttt) REVERT: C 332 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6975 (mtp180) REVERT: C 336 PHE cc_start: 0.6526 (m-80) cc_final: 0.6031 (m-80) REVERT: D 148 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7501 (mt) REVERT: D 218 ARG cc_start: 0.5367 (tmm-80) cc_final: 0.4652 (tmm-80) REVERT: D 331 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7060 (mt) REVERT: E 42 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7788 (t) REVERT: E 125 TYR cc_start: 0.8124 (t80) cc_final: 0.7666 (t80) REVERT: E 131 PHE cc_start: 0.6262 (m-80) cc_final: 0.5875 (m-80) REVERT: E 176 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: F 144 ASN cc_start: 0.5901 (m110) cc_final: 0.5385 (m110) REVERT: M 71 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7076 (mt-10) outliers start: 93 outliers final: 62 residues processed: 378 average time/residue: 0.1324 time to fit residues: 72.9735 Evaluate side-chains 383 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 312 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 269 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 204 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 72 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 329 ASN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 223 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.214628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187563 restraints weight = 19495.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189970 restraints weight = 17336.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.191689 restraints weight = 12248.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192187 restraints weight = 9423.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.192447 restraints weight = 8610.140| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15710 Z= 0.173 Angle : 0.907 17.626 21627 Z= 0.455 Chirality : 0.047 0.412 2615 Planarity : 0.006 0.082 2759 Dihedral : 17.294 175.421 2768 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.65 % Favored : 84.91 % Rotamer: Outliers : 4.64 % Allowed : 20.34 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.56 (0.16), residues: 2055 helix: -1.65 (0.23), residues: 454 sheet: -3.51 (0.24), residues: 250 loop : -3.68 (0.14), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 314 TYR 0.017 0.001 TYR N 20 PHE 0.015 0.002 PHE F 176 TRP 0.045 0.003 TRP C 270 HIS 0.008 0.002 HIS D 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (15710) covalent geometry : angle 0.90668 / 0.45 (21627) hydrogen bonds : bond 0.03701 / 2.55 ( 415) hydrogen bonds : angle 7.09628 / 4.85 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6013 (mt0) cc_final: 0.5767 (tt0) REVERT: A 144 ASN cc_start: 0.4097 (m-40) cc_final: 0.3344 (m-40) REVERT: A 314 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.4525 (ttp80) REVERT: A 332 ARG cc_start: 0.7940 (mtp85) cc_final: 0.6087 (ttp80) REVERT: B 91 LEU cc_start: 0.7897 (mt) cc_final: 0.7686 (mt) REVERT: B 148 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 197 GLU cc_start: 0.7059 (pm20) cc_final: 0.6837 (pm20) REVERT: B 239 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7795 (mttt) REVERT: B 293 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7530 (mmtm) REVERT: C 58 LYS cc_start: 0.6964 (mttt) cc_final: 0.6514 (mttt) REVERT: C 158 VAL cc_start: 0.8171 (t) cc_final: 0.7669 (p) REVERT: D 179 LEU cc_start: 0.7789 (mt) cc_final: 0.7523 (tp) REVERT: D 218 ARG cc_start: 0.5139 (tmm-80) cc_final: 0.4448 (tmm-80) REVERT: D 258 GLN cc_start: 0.5865 (OUTLIER) cc_final: 0.5567 (tt0) REVERT: D 331 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6798 (mt) REVERT: E 42 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (t) REVERT: E 125 TYR cc_start: 0.8027 (t80) cc_final: 0.7522 (t80) REVERT: E 131 PHE cc_start: 0.5887 (m-80) cc_final: 0.5565 (m-80) REVERT: E 176 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.5539 (m-10) REVERT: F 46 GLU cc_start: 0.6768 (tt0) cc_final: 0.6554 (tt0) REVERT: F 144 ASN cc_start: 0.5487 (m110) cc_final: 0.4967 (m110) REVERT: N 51 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7290 (mm-30) REVERT: M 71 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7120 (mt-10) outliers start: 63 outliers final: 45 residues processed: 355 average time/residue: 0.1326 time to fit residues: 68.7656 Evaluate side-chains 356 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 305 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 190 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 overall best weight: 0.8638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 329 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.220924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.198298 restraints weight = 19032.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198899 restraints weight = 21096.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.200765 restraints weight = 15256.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.201273 restraints weight = 11805.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.201535 restraints weight = 10521.279| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15710 Z= 0.154 Angle : 0.858 15.171 21627 Z= 0.432 Chirality : 0.045 0.390 2615 Planarity : 0.006 0.088 2759 Dihedral : 16.998 174.495 2768 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.44 % Allowed : 16.06 % Favored : 83.50 % Rotamer: Outliers : 3.46 % Allowed : 21.59 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.40 (0.16), residues: 2055 helix: -1.41 (0.24), residues: 459 sheet: -3.40 (0.23), residues: 307 loop : -3.59 (0.15), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 161 TYR 0.017 0.001 TYR M 20 PHE 0.014 0.002 PHE F 176 TRP 0.036 0.002 TRP C 270 HIS 0.005 0.001 HIS C 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (15710) covalent geometry : angle 0.85796 / 0.43 (21627) hydrogen bonds : bond 0.03374 / 2.33 ( 415) hydrogen bonds : angle 6.75297 / 4.62 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.5949 (mt0) cc_final: 0.5694 (tt0) REVERT: A 128 ASP cc_start: 0.7935 (t0) cc_final: 0.7524 (m-30) REVERT: B 148 LEU cc_start: 0.7361 (mt) cc_final: 0.7159 (tp) REVERT: B 239 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7774 (mttt) REVERT: B 329 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6668 (t0) REVERT: C 58 LYS cc_start: 0.6920 (mttt) cc_final: 0.6589 (mttt) REVERT: C 158 VAL cc_start: 0.8110 (t) cc_final: 0.7504 (p) REVERT: D 148 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6885 (tp) REVERT: D 179 LEU cc_start: 0.7628 (mt) cc_final: 0.7419 (tp) REVERT: E 42 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7700 (t) REVERT: E 125 TYR cc_start: 0.7860 (t80) cc_final: 0.7401 (t80) REVERT: E 131 PHE cc_start: 0.5682 (m-80) cc_final: 0.5426 (m-80) REVERT: F 84 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5466 (tp) REVERT: F 144 ASN cc_start: 0.5329 (m110) cc_final: 0.4909 (m110) REVERT: N 51 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7175 (mm-30) REVERT: N 53 TRP cc_start: 0.7245 (p-90) cc_final: 0.6916 (p-90) REVERT: M 71 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7104 (mt-10) outliers start: 47 outliers final: 35 residues processed: 342 average time/residue: 0.1274 time to fit residues: 63.9736 Evaluate side-chains 339 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 179 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 163 ASN B 310 ASN B 329 ASN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 110 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.215635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189353 restraints weight = 19601.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.190122 restraints weight = 16243.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191941 restraints weight = 13070.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.193390 restraints weight = 9701.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.193502 restraints weight = 8741.242| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15710 Z= 0.189 Angle : 0.893 16.276 21627 Z= 0.445 Chirality : 0.047 0.420 2615 Planarity : 0.007 0.128 2759 Dihedral : 16.976 173.873 2768 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.49 % Allowed : 16.35 % Favored : 83.16 % Rotamer: Outliers : 3.54 % Allowed : 21.96 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.45 (0.16), residues: 2055 helix: -1.54 (0.23), residues: 475 sheet: -3.40 (0.23), residues: 307 loop : -3.61 (0.15), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 265 TYR 0.015 0.001 TYR N 20 PHE 0.015 0.002 PHE A 131 TRP 0.055 0.003 TRP C 270 HIS 0.011 0.002 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (15710) covalent geometry : angle 0.89330 / 0.44 (21627) hydrogen bonds : bond 0.03435 / 2.36 ( 415) hydrogen bonds : angle 6.70344 / 4.59 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 300 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.6204 (mt0) cc_final: 0.5939 (tt0) REVERT: A 128 ASP cc_start: 0.8214 (t0) cc_final: 0.7550 (m-30) REVERT: B 239 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7779 (mttt) REVERT: B 329 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.7135 (t0) REVERT: C 58 LYS cc_start: 0.6916 (mttt) cc_final: 0.6600 (mttt) REVERT: C 158 VAL cc_start: 0.8162 (t) cc_final: 0.7536 (p) REVERT: D 148 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7035 (tp) REVERT: E 42 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7659 (t) REVERT: E 125 TYR cc_start: 0.8043 (t80) cc_final: 0.7536 (t80) REVERT: E 131 PHE cc_start: 0.5950 (m-80) cc_final: 0.5606 (m-80) REVERT: F 84 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5380 (tp) REVERT: F 105 THR cc_start: 0.6113 (p) cc_final: 0.5818 (p) REVERT: F 144 ASN cc_start: 0.5518 (m110) cc_final: 0.4994 (m110) REVERT: N 51 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7415 (mm-30) REVERT: M 71 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7105 (mt-10) outliers start: 48 outliers final: 38 residues processed: 330 average time/residue: 0.1301 time to fit residues: 62.2734 Evaluate side-chains 341 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 329 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 66 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 152 optimal weight: 0.0270 chunk 174 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 199 optimal weight: 0.0020 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 110 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.212886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.185330 restraints weight = 19883.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.186299 restraints weight = 16826.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.188017 restraints weight = 13119.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.189263 restraints weight = 10195.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189413 restraints weight = 9375.748| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15710 Z= 0.222 Angle : 0.923 17.035 21627 Z= 0.461 Chirality : 0.049 0.455 2615 Planarity : 0.007 0.123 2759 Dihedral : 17.010 173.303 2768 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.49 % Allowed : 18.88 % Favored : 80.63 % Rotamer: Outliers : 3.98 % Allowed : 21.74 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.45 (0.16), residues: 2055 helix: -1.51 (0.24), residues: 463 sheet: -3.34 (0.23), residues: 307 loop : -3.63 (0.15), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 56 TYR 0.017 0.002 TYR A 305 PHE 0.017 0.002 PHE B 147 TRP 0.062 0.003 TRP C 270 HIS 0.008 0.002 HIS B 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (15710) covalent geometry : angle 0.92321 / 0.46 (21627) hydrogen bonds : bond 0.03598 / 2.47 ( 415) hydrogen bonds : angle 6.74239 / 4.62 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.88 seconds wall clock time: 45 minutes 4.49 seconds (2704.49 seconds total)