Starting phenix.real_space_refine on Sat Aug 23 23:39:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_6729_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_6729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_6729.map" model { file = "/net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_6729_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xlo_6729/08_2025/5xlo_6729_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.34, per 1000 atoms: 0.22 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: 0.91 Conformation dependent library (CDL) restraints added in 607.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.45 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: 1.57 Time building geometry restraints manager: 1.29 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=" CB GLN A 37 " pdb=" CG GLN A 37 " ideal model delta sigma weight residual 1.520 1.436 0.084 3.00e-02 1.11e+03 7.85e+00 bond pdb=" CB GLN F 37 " pdb=" CG GLN F 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.71e+00 bond pdb=" CB GLN C 37 " pdb=" CG GLN C 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.68e+00 bond pdb=" CB GLN B 37 " pdb=" CG GLN B 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.66e+00 bond pdb=" CB GLN D 37 " pdb=" CG GLN D 37 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.64e+00 ... (remaining 15705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 20665 2.88 - 5.75: 778 5.75 - 8.63: 121 8.63 - 11.50: 51 11.50 - 14.38: 12 Bond angle restraints: 21627 Sorted by residual: angle pdb=" C4' A K 4 " pdb=" C3' A K 4 " pdb=" O3' A K 4 " ideal model delta sigma weight residual 109.40 117.56 -8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" N GLY M 40 " pdb=" CA GLY M 40 " pdb=" C GLY M 40 " ideal model delta sigma weight residual 111.36 117.52 -6.16 1.17e+00 7.31e-01 2.77e+01 angle pdb=" N GLY N 40 " pdb=" CA GLY N 40 " pdb=" C GLY N 40 " ideal model delta sigma weight residual 111.36 117.51 -6.15 1.17e+00 7.31e-01 2.76e+01 angle pdb=" C HIS N 11 " pdb=" N LEU N 12 " pdb=" CA LEU N 12 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 angle pdb=" C HIS M 11 " pdb=" N LEU M 12 " pdb=" CA LEU M 12 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.59e+01 ... (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: 2247 0.086 - 0.172: 330 0.172 - 0.258: 28 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.210 Find NCS groups from input model: 0.280 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 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= 0.404 Angle : 1.367 14.376 21627 Z= 0.701 Chirality : 0.064 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 aren 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 covalent geometry : bond 0.00909 (15710) covalent geometry : angle 1.36743 (21627) hydrogen bonds : bond 0.19711 ( 415) hydrogen bonds : angle 13.61624 ( 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 : 0.348 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: 0.6402 (tt) REVERT: A 270 TRP cc_start: 0.6527 (t-100) cc_final: 0.6034 (t-100) REVERT: B 24 LEU cc_start: 0.8048 (mp) cc_final: 0.7611 (mp) REVERT: B 214 VAL cc_start: 0.7705 (t) cc_final: 0.7378 (p) REVERT: B 332 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7655 (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: 0.6647 (mttt) REVERT: C 91 LEU cc_start: 0.7295 (mt) cc_final: 0.6497 (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: 0.6395 (t0) REVERT: D 267 ILE cc_start: 0.8047 (mt) cc_final: 0.7812 (mt) REVERT: E 25 MET cc_start: 0.4921 (mmm) cc_final: 0.4522 (mmm) REVERT: E 125 TYR cc_start: 0.6944 (t80) cc_final: 0.6289 (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: 0.4879 (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: 0.6243 (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: 0.1169 time to fit residues: 75.9186 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 : 0.431 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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** B 310 ASN C 110 ASN C 141 ASN C 144 ASN C 223 GLN C 256 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN E 72 GLN E 110 ASN E 223 GLN E 256 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN F 72 GLN F 110 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.226462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.202962 restraints weight = 19280.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.203620 restraints weight = 20019.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.205394 restraints weight = 15355.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.207074 restraints weight = 11182.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.207155 restraints weight = 10314.818| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15710 Z= 0.164 Angle : 0.864 13.118 21627 Z= 0.439 Chirality : 0.044 0.208 2615 Planarity : 0.006 0.084 2759 Dihedral : 17.478 176.307 2770 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.70 % Favored : 86.76 % Rotamer: Outliers : 3.76 % Allowed : 11.79 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.90 (0.14), residues: 2055 helix: -2.40 (0.19), residues: 442 sheet: -3.52 (0.23), residues: 290 loop : -3.73 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 265 TYR 0.016 0.002 TYR D 125 PHE 0.021 0.002 PHE A 131 TRP 0.024 0.002 TRP N 53 HIS 0.016 0.002 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00351 (15710) covalent geometry : angle 0.86400 (21627) hydrogen bonds : bond 0.04010 ( 415) hydrogen bonds : angle 8.09017 ( 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: 51 poor density : 370 time to evaluate : 0.436 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: A 32 GLN cc_start: 0.6286 (mt0) cc_final: 0.5931 (tt0) REVERT: A 131 PHE cc_start: 0.6829 (m-80) cc_final: 0.6182 (m-80) REVERT: A 270 TRP cc_start: 0.6192 (t-100) cc_final: 0.5715 (t-100) REVERT: A 332 ARG cc_start: 0.7814 (mtp85) cc_final: 0.5889 (ttp80) REVERT: B 169 GLU cc_start: 0.5812 (tt0) cc_final: 0.5320 (pt0) REVERT: B 239 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7630 (mttt) REVERT: B 314 ARG cc_start: 0.7887 (mmm160) cc_final: 0.6845 (tpt90) REVERT: C 58 LYS cc_start: 0.7196 (mttt) cc_final: 0.6716 (mttt) REVERT: C 295 TYR cc_start: 0.8059 (m-80) cc_final: 0.7802 (m-80) REVERT: D 46 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6180 (tm-30) REVERT: D 218 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.4916 (tmm-80) REVERT: D 234 ASP cc_start: 0.7000 (m-30) cc_final: 0.6734 (t0) REVERT: E 25 MET cc_start: 0.4386 (mmm) cc_final: 0.3855 (mmm) REVERT: E 42 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7391 (t) REVERT: E 125 TYR cc_start: 0.7381 (t80) cc_final: 0.6968 (t80) REVERT: F 58 LYS cc_start: 0.7125 (mttt) cc_final: 0.6919 (mttt) REVERT: F 163 ASN cc_start: 0.8070 (m-40) cc_final: 0.7818 (m-40) REVERT: N 53 TRP cc_start: 0.6477 (p-90) cc_final: 0.6103 (t60) REVERT: N 65 ILE cc_start: 0.8562 (mp) cc_final: 0.8334 (mt) REVERT: M 29 ARG cc_start: 0.7162 (ttp-170) cc_final: 0.6945 (ptm160) outliers start: 51 outliers final: 22 residues processed: 397 average time/residue: 0.1170 time to fit residues: 66.6300 Evaluate side-chains 353 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 329 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 232 ILE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 237 ASP 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 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 218 ARG 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 F residue 42 VAL Chi-restraints excluded: chain F residue 43 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 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 323 GLN ** C 37 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** C 300 GLN D 256 HIS D 258 GLN ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.208717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181408 restraints weight = 19767.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181841 restraints weight = 17265.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183913 restraints weight = 14117.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184761 restraints weight = 10494.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184831 restraints weight = 9712.219| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.008 0.121 15710 Z= 0.353 Angle : 1.069 14.963 21627 Z= 0.543 Chirality : 0.050 0.333 2615 Planarity : 0.008 0.092 2759 Dihedral : 17.882 170.093 2770 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.49 % Allowed : 19.37 % Favored : 80.15 % Rotamer: Outliers : 5.82 % Allowed : 13.34 % Favored : 80.84 % 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 aren not related in a simple way. whole: -5.12 (0.15), residues: 2055 helix: -2.56 (0.20), residues: 467 sheet: -3.71 (0.22), residues: 333 loop : -3.84 (0.14), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 94 TYR 0.029 0.003 TYR D 125 PHE 0.039 0.003 PHE E 131 TRP 0.043 0.004 TRP C 270 HIS 0.011 0.002 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00788 (15710) covalent geometry : angle 1.06945 (21627) hydrogen bonds : bond 0.04846 ( 415) hydrogen bonds : angle 8.08805 ( 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 433 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 354 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TRP cc_start: 0.6579 (t-100) cc_final: 0.5665 (t-100) REVERT: A 305 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6648 (m-10) REVERT: A 338 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 169 GLU cc_start: 0.5754 (tt0) cc_final: 0.5305 (pt0) REVERT: B 197 GLU cc_start: 0.7227 (pm20) cc_final: 0.6991 (pm20) REVERT: B 218 ARG cc_start: 0.6586 (ttp80) cc_final: 0.5964 (ttp80) REVERT: B 239 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7503 (mttt) REVERT: B 336 PHE cc_start: 0.6665 (m-80) cc_final: 0.5965 (m-80) REVERT: C 25 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.5094 (mmm) REVERT: C 42 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8192 (t) REVERT: C 58 LYS cc_start: 0.7047 (mttt) cc_final: 0.6584 (mttt) REVERT: C 158 VAL cc_start: 0.8273 (t) cc_final: 0.7871 (p) REVERT: C 336 PHE cc_start: 0.6500 (m-80) cc_final: 0.6098 (m-80) REVERT: D 46 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 218 ARG cc_start: 0.5637 (OUTLIER) cc_final: 0.4709 (tmm-80) REVERT: D 270 TRP cc_start: 0.7071 (t-100) cc_final: 0.6845 (t-100) REVERT: E 25 MET cc_start: 0.5281 (mmm) cc_final: 0.4288 (mmm) REVERT: E 42 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7757 (t) REVERT: E 125 TYR cc_start: 0.8192 (t80) cc_final: 0.7769 (t80) REVERT: E 131 PHE cc_start: 0.6674 (m-80) cc_final: 0.6458 (m-80) REVERT: E 176 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: E 210 LEU cc_start: 0.6199 (OUTLIER) cc_final: 0.5884 (mt) REVERT: F 46 GLU cc_start: 0.7496 (tt0) cc_final: 0.7122 (tt0) REVERT: F 56 ARG cc_start: 0.6852 (ttt-90) cc_final: 0.6605 (mmm160) REVERT: F 58 LYS cc_start: 0.7292 (mttt) cc_final: 0.6994 (mttt) REVERT: F 148 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7193 (mm) REVERT: N 53 TRP cc_start: 0.7376 (p-90) cc_final: 0.7002 (p-90) REVERT: N 71 GLU cc_start: 0.8204 (tp30) cc_final: 0.7977 (tp30) outliers start: 79 outliers final: 42 residues processed: 401 average time/residue: 0.1157 time to fit residues: 66.5977 Evaluate side-chains 366 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 316 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 305 TYR 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 147 PHE Chi-restraints excluded: chain B residue 199 ILE 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 C residue 25 MET Chi-restraints excluded: chain C residue 42 VAL 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 76 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 268 ASP 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 210 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 293 LYS 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 97 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 53 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 195 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN A 241 GLN B 163 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 323 GLN B 324 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 258 GLN D 324 HIS ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 110 ASN F 144 ASN F 256 HIS M 49 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.218991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.195812 restraints weight = 19327.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.196105 restraints weight = 20948.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197842 restraints weight = 16410.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198219 restraints weight = 11848.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.198547 restraints weight = 11717.302| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15710 Z= 0.151 Angle : 0.820 15.297 21627 Z= 0.416 Chirality : 0.043 0.215 2615 Planarity : 0.006 0.070 2759 Dihedral : 17.166 178.328 2770 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.14 % Favored : 86.37 % Rotamer: Outliers : 4.72 % Allowed : 17.83 % Favored : 77.45 % 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 aren not related in a simple way. whole: -4.61 (0.15), residues: 2055 helix: -1.70 (0.23), residues: 457 sheet: -3.52 (0.23), residues: 307 loop : -3.68 (0.14), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 314 TYR 0.015 0.001 TYR N 20 PHE 0.025 0.002 PHE E 131 TRP 0.039 0.003 TRP C 270 HIS 0.007 0.001 HIS E 324 Details of bonding type rmsd covalent geometry : bond 0.00328 (15710) covalent geometry : angle 0.82027 (21627) hydrogen bonds : bond 0.03333 ( 415) hydrogen bonds : angle 7.06268 ( 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 411 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 347 time to evaluate : 0.482 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: A 218 ARG cc_start: 0.4798 (ttp-170) cc_final: 0.4396 (ttp-170) REVERT: A 332 ARG cc_start: 0.7737 (mtp85) cc_final: 0.6271 (ttp80) REVERT: B 169 GLU cc_start: 0.5717 (tt0) cc_final: 0.5388 (pt0) REVERT: B 174 TRP cc_start: 0.7918 (t60) cc_final: 0.7490 (t60) REVERT: B 219 ILE cc_start: 0.7740 (pt) cc_final: 0.7076 (pt) REVERT: B 239 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7703 (mttt) REVERT: B 330 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7734 (tt) REVERT: C 42 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7997 (t) REVERT: C 58 LYS cc_start: 0.6950 (mttt) cc_final: 0.6603 (mttt) REVERT: C 314 ARG cc_start: 0.6055 (tmt170) cc_final: 0.5797 (tmt170) REVERT: D 46 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7109 (tm-30) REVERT: D 218 ARG cc_start: 0.5502 (tmm-80) cc_final: 0.5187 (tmm-80) REVERT: D 323 GLN cc_start: 0.7932 (pt0) cc_final: 0.7570 (pt0) REVERT: E 25 MET cc_start: 0.5074 (mmm) cc_final: 0.4039 (mmm) REVERT: E 42 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7678 (t) REVERT: E 125 TYR cc_start: 0.7740 (t80) cc_final: 0.7355 (t80) REVERT: E 131 PHE cc_start: 0.6168 (m-80) cc_final: 0.5878 (m-80) REVERT: E 210 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5582 (mt) REVERT: F 46 GLU cc_start: 0.6866 (tt0) cc_final: 0.6599 (tt0) REVERT: F 105 THR cc_start: 0.6387 (p) cc_final: 0.5962 (t) REVERT: F 223 GLN cc_start: 0.5334 (mt0) cc_final: 0.4970 (mt0) REVERT: F 330 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.5215 (tt) REVERT: N 15 MET cc_start: 0.5844 (mtp) cc_final: 0.5566 (mtm) REVERT: N 53 TRP cc_start: 0.7244 (p-90) cc_final: 0.6841 (p-90) outliers start: 64 outliers final: 34 residues processed: 387 average time/residue: 0.1238 time to fit residues: 68.1876 Evaluate side-chains 354 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 93 VAL 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 67 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE 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: 9.9990 chunk 117 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 121 optimal weight: 0.0170 chunk 94 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 202 optimal weight: 0.0270 chunk 79 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 256 HIS B 310 ASN C 141 ASN C 144 ASN C 300 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 322 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.223309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.205856 restraints weight = 19098.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.205470 restraints weight = 21966.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.205785 restraints weight = 18788.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.205237 restraints weight = 17741.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206212 restraints weight = 14704.574| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15710 Z= 0.153 Angle : 0.801 14.602 21627 Z= 0.403 Chirality : 0.043 0.217 2615 Planarity : 0.006 0.080 2759 Dihedral : 16.896 177.549 2770 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.34 % Allowed : 15.33 % Favored : 84.33 % Rotamer: Outliers : 5.16 % Allowed : 17.39 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.16), residues: 2055 helix: -1.31 (0.24), residues: 469 sheet: -3.31 (0.24), residues: 307 loop : -3.58 (0.15), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 218 TYR 0.013 0.001 TYR N 20 PHE 0.019 0.002 PHE E 131 TRP 0.038 0.002 TRP C 270 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00333 (15710) covalent geometry : angle 0.80139 (21627) hydrogen bonds : bond 0.03142 ( 415) hydrogen bonds : angle 6.64548 ( 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 385 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 315 time to evaluate : 0.548 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 270 TRP cc_start: 0.5867 (t-100) cc_final: 0.4874 (t-100) REVERT: B 239 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7414 (mttt) REVERT: B 330 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7677 (tt) REVERT: C 42 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7801 (t) REVERT: C 58 LYS cc_start: 0.6909 (mttt) cc_final: 0.6612 (mttt) REVERT: C 239 LYS cc_start: 0.8557 (mtpt) cc_final: 0.8186 (mtpp) REVERT: D 46 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7016 (tm-30) REVERT: D 176 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: D 218 ARG cc_start: 0.5694 (OUTLIER) cc_final: 0.5197 (tmm-80) REVERT: D 323 GLN cc_start: 0.7690 (pt0) cc_final: 0.7386 (pt0) REVERT: E 25 MET cc_start: 0.4927 (mmm) cc_final: 0.3897 (mmm) REVERT: E 42 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7632 (t) REVERT: E 125 TYR cc_start: 0.7607 (t80) cc_final: 0.7265 (t80) REVERT: E 210 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5269 (mt) REVERT: F 46 GLU cc_start: 0.6912 (tt0) cc_final: 0.6648 (tt0) REVERT: F 105 THR cc_start: 0.6559 (p) cc_final: 0.6273 (t) REVERT: F 322 GLN cc_start: 0.7177 (pt0) cc_final: 0.6972 (pt0) REVERT: F 330 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5428 (tt) REVERT: N 53 TRP cc_start: 0.7269 (p-90) cc_final: 0.6846 (p-90) REVERT: M 29 ARG cc_start: 0.7241 (ttp-170) cc_final: 0.6964 (mtp85) outliers start: 70 outliers final: 45 residues processed: 351 average time/residue: 0.1222 time to fit residues: 61.5897 Evaluate side-chains 353 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 312 VAL 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 100 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 42 VAL 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 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 59 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 210 LEU 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 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU 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: 8.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.0970 chunk 88 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN C 300 GLN ** D 32 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 ** 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 = 0.4324 r_free = 0.4324 target = 0.212280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.185878 restraints weight = 19532.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186665 restraints weight = 15766.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187673 restraints weight = 12636.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188114 restraints weight = 10966.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188487 restraints weight = 10188.030| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 15710 Z= 0.224 Angle : 0.877 15.456 21627 Z= 0.442 Chirality : 0.046 0.264 2615 Planarity : 0.006 0.080 2759 Dihedral : 17.078 175.826 2770 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.03 % Favored : 82.58 % Rotamer: Outliers : 5.38 % Allowed : 18.20 % Favored : 76.42 % 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 aren not related in a simple way. whole: -4.40 (0.16), residues: 2055 helix: -1.47 (0.24), residues: 457 sheet: -3.36 (0.23), residues: 326 loop : -3.56 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 56 TYR 0.015 0.002 TYR A 305 PHE 0.045 0.002 PHE E 131 TRP 0.031 0.003 TRP C 270 HIS 0.008 0.002 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00505 (15710) covalent geometry : angle 0.87729 (21627) hydrogen bonds : bond 0.03646 ( 415) hydrogen bonds : angle 6.77612 ( 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 394 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TRP cc_start: 0.6305 (t-100) cc_final: 0.5416 (t-100) REVERT: B 44 VAL cc_start: 0.8948 (t) cc_final: 0.8747 (m) REVERT: B 239 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7541 (mttt) REVERT: B 314 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7049 (mmm160) REVERT: C 42 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8022 (t) REVERT: C 58 LYS cc_start: 0.6977 (mttt) cc_final: 0.6570 (mttt) REVERT: C 174 TRP cc_start: 0.7665 (t60) cc_final: 0.7413 (t60) REVERT: D 46 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 206 SER cc_start: 0.8589 (m) cc_final: 0.8354 (t) REVERT: D 218 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5091 (tmm-80) REVERT: E 25 MET cc_start: 0.4713 (mmm) cc_final: 0.3715 (mmm) REVERT: E 42 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (t) REVERT: E 125 TYR cc_start: 0.8170 (t80) cc_final: 0.7726 (t80) REVERT: E 176 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6254 (m-10) REVERT: E 210 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5779 (mt) REVERT: F 46 GLU cc_start: 0.7349 (tt0) cc_final: 0.6986 (tt0) REVERT: F 148 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7136 (mm) REVERT: F 163 ASN cc_start: 0.8432 (m-40) cc_final: 0.8134 (m110) REVERT: F 280 ILE cc_start: 0.6192 (OUTLIER) cc_final: 0.5910 (pt) REVERT: N 53 TRP cc_start: 0.7534 (p-90) cc_final: 0.7070 (p-90) REVERT: M 29 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6945 (ptm160) outliers start: 73 outliers final: 50 residues processed: 363 average time/residue: 0.1257 time to fit residues: 65.4405 Evaluate side-chains 366 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 308 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 147 PHE Chi-restraints excluded: chain B residue 176 PHE 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 C residue 42 VAL 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 162 ILE 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 58 LYS Chi-restraints excluded: chain D residue 76 LEU 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 218 ARG Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 210 LEU 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 72 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE 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: 6.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 241 GLN B 129 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 258 GLN B 310 ASN B 329 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 300 GLN D 258 GLN D 323 GLN ** E 223 GLN ** 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 F 144 ASN F 241 GLN F 258 GLN F 322 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.204724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178494 restraints weight = 19735.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.177949 restraints weight = 19495.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179261 restraints weight = 15802.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180961 restraints weight = 13434.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181301 restraints weight = 11030.003| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 15710 Z= 0.348 Angle : 1.071 17.585 21627 Z= 0.541 Chirality : 0.052 0.332 2615 Planarity : 0.008 0.095 2759 Dihedral : 17.562 169.826 2770 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 20.58 % Favored : 79.03 % Rotamer: Outliers : 6.71 % Allowed : 18.20 % Favored : 75.09 % 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 aren not related in a simple way. whole: -4.93 (0.15), residues: 2055 helix: -2.00 (0.23), residues: 453 sheet: -3.74 (0.21), residues: 380 loop : -3.80 (0.14), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 94 TYR 0.023 0.003 TYR B 125 PHE 0.043 0.004 PHE E 131 TRP 0.036 0.004 TRP B 270 HIS 0.016 0.003 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00782 (15710) covalent geometry : angle 1.07124 (21627) hydrogen bonds : bond 0.04715 ( 415) hydrogen bonds : angle 7.31784 ( 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 419 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TRP cc_start: 0.6735 (t-100) cc_final: 0.5933 (t-100) REVERT: B 25 MET cc_start: 0.7522 (tpt) cc_final: 0.7151 (tpt) REVERT: B 239 LYS cc_start: 0.8444 (mtmt) cc_final: 0.7925 (mttt) REVERT: B 314 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7013 (mmm160) REVERT: B 330 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7657 (tt) REVERT: B 336 PHE cc_start: 0.6451 (m-80) cc_final: 0.6067 (m-80) REVERT: C 25 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.4948 (mmm) REVERT: C 42 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8258 (t) REVERT: C 58 LYS cc_start: 0.7042 (mttt) cc_final: 0.6563 (mttt) REVERT: C 314 ARG cc_start: 0.7284 (tmt170) cc_final: 0.6856 (tmt170) REVERT: C 332 ARG cc_start: 0.7523 (mtp180) cc_final: 0.7133 (mtp180) REVERT: C 336 PHE cc_start: 0.6603 (m-80) cc_final: 0.6046 (m-80) REVERT: D 148 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.6549 (tt) REVERT: D 206 SER cc_start: 0.8952 (m) cc_final: 0.8550 (t) REVERT: D 293 LYS cc_start: 0.8487 (mttp) cc_final: 0.8268 (mttp) REVERT: E 25 MET cc_start: 0.5045 (mmm) cc_final: 0.3804 (mmm) REVERT: E 42 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7816 (t) REVERT: E 125 TYR cc_start: 0.8586 (t80) cc_final: 0.8318 (t80) REVERT: E 129 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7794 (tp40) REVERT: E 176 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: E 210 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6366 (mt) REVERT: E 280 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6817 (pt) REVERT: F 105 THR cc_start: 0.6019 (p) cc_final: 0.5613 (t) REVERT: N 66 GLU cc_start: 0.7592 (tt0) cc_final: 0.7372 (tt0) outliers start: 91 outliers final: 54 residues processed: 378 average time/residue: 0.1188 time to fit residues: 64.4978 Evaluate side-chains 381 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 318 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 199 ILE 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 329 ASN Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 42 VAL 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 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 93 VAL 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 218 ARG Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 280 ILE 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 144 ASN Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE 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: 0.9980 chunk 134 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 329 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN C 300 GLN D 323 GLN ** E 72 GLN ** 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 F 144 ASN F 151 ASN F 258 GLN F 322 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.210310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184504 restraints weight = 19856.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184408 restraints weight = 17330.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.185721 restraints weight = 13921.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186226 restraints weight = 11578.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.186640 restraints weight = 10700.065| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15710 Z= 0.205 Angle : 0.909 16.674 21627 Z= 0.455 Chirality : 0.046 0.398 2615 Planarity : 0.006 0.094 2759 Dihedral : 17.167 178.831 2770 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.25 % Favored : 83.36 % Rotamer: Outliers : 5.08 % Allowed : 21.00 % Favored : 73.91 % 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 aren not related in a simple way. whole: -4.68 (0.16), residues: 2055 helix: -1.71 (0.23), residues: 463 sheet: -3.67 (0.21), residues: 346 loop : -3.68 (0.15), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 94 TYR 0.017 0.002 TYR M 6 PHE 0.041 0.002 PHE E 131 TRP 0.026 0.003 TRP B 270 HIS 0.008 0.002 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00459 (15710) covalent geometry : angle 0.90858 (21627) hydrogen bonds : bond 0.03659 ( 415) hydrogen bonds : angle 6.68651 ( 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 405 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 0.472 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: A 270 TRP cc_start: 0.6338 (t-100) cc_final: 0.5543 (t-100) REVERT: B 239 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7542 (mttt) REVERT: B 314 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7595 (tpt90) REVERT: C 25 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.4908 (mmm) REVERT: C 42 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (t) REVERT: C 58 LYS cc_start: 0.6982 (mttt) cc_final: 0.6534 (mttt) REVERT: C 265 ARG cc_start: 0.7287 (ttp-110) cc_final: 0.6582 (mtt90) REVERT: C 314 ARG cc_start: 0.6999 (tmt170) cc_final: 0.6643 (tmt170) REVERT: C 332 ARG cc_start: 0.7342 (mtp180) cc_final: 0.7093 (mtp180) REVERT: D 72 GLN cc_start: 0.5007 (OUTLIER) cc_final: 0.3406 (mm-40) REVERT: E 25 MET cc_start: 0.5018 (mmm) cc_final: 0.3924 (mmm) REVERT: E 42 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7823 (t) REVERT: E 125 TYR cc_start: 0.8465 (t80) cc_final: 0.8117 (t80) REVERT: E 176 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5020 (m-10) REVERT: E 210 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6180 (mt) REVERT: E 280 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6757 (pt) REVERT: E 293 LYS cc_start: 0.7785 (tttp) cc_final: 0.7520 (tttm) REVERT: F 46 GLU cc_start: 0.7266 (tt0) cc_final: 0.6925 (tt0) REVERT: F 105 THR cc_start: 0.5433 (p) cc_final: 0.4728 (t) REVERT: F 144 ASN cc_start: 0.5690 (m110) cc_final: 0.4770 (m110) REVERT: F 223 GLN cc_start: 0.5381 (mt0) cc_final: 0.4907 (mt0) REVERT: M 32 ASN cc_start: 0.7481 (m-40) cc_final: 0.6368 (p0) outliers start: 69 outliers final: 48 residues processed: 376 average time/residue: 0.1233 time to fit residues: 66.4322 Evaluate side-chains 371 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 221 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 280 ILE 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 25 MET Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 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 72 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 79 VAL 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 218 ARG Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 300 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 53 TRP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE 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: 4.9990 chunk 135 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 201 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 258 GLN B 310 ASN B 323 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 151 ASN D 323 GLN D 329 ASN ** E 72 GLN ** 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 F 241 GLN F 322 GLN N 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.212791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.187709 restraints weight = 19669.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186795 restraints weight = 18487.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188720 restraints weight = 15282.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.190082 restraints weight = 11550.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190294 restraints weight = 10125.311| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15710 Z= 0.191 Angle : 0.884 16.061 21627 Z= 0.442 Chirality : 0.045 0.340 2615 Planarity : 0.006 0.097 2759 Dihedral : 17.003 177.240 2770 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 17.76 % Favored : 81.85 % Rotamer: Outliers : 4.79 % Allowed : 22.25 % Favored : 72.96 % 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 aren not related in a simple way. whole: -4.60 (0.16), residues: 2055 helix: -1.60 (0.24), residues: 458 sheet: -3.74 (0.21), residues: 379 loop : -3.57 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 218 TYR 0.017 0.002 TYR M 6 PHE 0.040 0.002 PHE E 131 TRP 0.033 0.003 TRP E 270 HIS 0.008 0.002 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00430 (15710) covalent geometry : angle 0.88423 (21627) hydrogen bonds : bond 0.03547 ( 415) hydrogen bonds : angle 6.49444 ( 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 393 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 328 time to evaluate : 0.403 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 270 TRP cc_start: 0.6333 (t-100) cc_final: 0.5541 (t-100) REVERT: B 239 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7495 (mttt) REVERT: B 314 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7616 (tpt90) REVERT: C 25 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.4835 (mmm) REVERT: C 42 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8036 (t) REVERT: C 58 LYS cc_start: 0.7033 (mttt) cc_final: 0.6631 (mttt) REVERT: C 94 ARG cc_start: 0.7213 (tpp80) cc_final: 0.6952 (ttm170) REVERT: C 174 TRP cc_start: 0.7469 (t60) cc_final: 0.7264 (t60) REVERT: C 218 ARG cc_start: 0.6893 (ttp80) cc_final: 0.6535 (tmm-80) REVERT: C 265 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6278 (mtt90) REVERT: C 314 ARG cc_start: 0.6999 (tmt170) cc_final: 0.6618 (tmt170) REVERT: D 72 GLN cc_start: 0.4977 (OUTLIER) cc_final: 0.3363 (mm-40) REVERT: D 148 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6914 (tp) REVERT: D 197 GLU cc_start: 0.6359 (mp0) cc_final: 0.6011 (mp0) REVERT: D 331 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6849 (mt) REVERT: E 25 MET cc_start: 0.5037 (mmm) cc_final: 0.3872 (mmm) REVERT: E 42 VAL cc_start: 0.8074 (OUTLIER) cc_final: 0.7823 (t) REVERT: E 125 TYR cc_start: 0.8311 (t80) cc_final: 0.7958 (t80) REVERT: E 129 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7753 (tp40) REVERT: E 176 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.4689 (m-10) REVERT: E 280 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6663 (pt) REVERT: F 46 GLU cc_start: 0.7201 (tt0) cc_final: 0.7001 (tm-30) REVERT: F 67 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.3997 (pp) REVERT: F 105 THR cc_start: 0.5876 (p) cc_final: 0.4943 (t) REVERT: F 223 GLN cc_start: 0.5156 (mt0) cc_final: 0.4748 (mt0) REVERT: M 29 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.7052 (ptm160) REVERT: M 32 ASN cc_start: 0.7245 (m-40) cc_final: 0.6038 (p0) outliers start: 65 outliers final: 47 residues processed: 363 average time/residue: 0.1248 time to fit residues: 64.9619 Evaluate side-chains 377 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 321 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 PHE 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 C residue 25 MET Chi-restraints excluded: chain C residue 42 VAL 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 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 72 GLN 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 218 ARG 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 44 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 176 PHE Chi-restraints excluded: chain E residue 280 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 67 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 53 TRP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE 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: 6.9990 chunk 121 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 204 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 310 ASN B 329 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 329 ASN ** E 72 GLN ** 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 F 144 ASN F 241 GLN F 322 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.219212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194456 restraints weight = 19454.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.193863 restraints weight = 17364.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.195910 restraints weight = 14158.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196688 restraints weight = 10508.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196917 restraints weight = 9456.496| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15710 Z= 0.143 Angle : 0.827 14.601 21627 Z= 0.415 Chirality : 0.043 0.331 2615 Planarity : 0.006 0.098 2759 Dihedral : 16.649 179.122 2770 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.72 % Favored : 85.89 % Rotamer: Outliers : 3.98 % Allowed : 23.43 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.16), residues: 2055 helix: -1.23 (0.25), residues: 463 sheet: -3.52 (0.22), residues: 332 loop : -3.48 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 218 TYR 0.016 0.001 TYR M 6 PHE 0.038 0.002 PHE E 131 TRP 0.038 0.003 TRP E 270 HIS 0.005 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00314 (15710) covalent geometry : angle 0.82675 (21627) hydrogen bonds : bond 0.03099 ( 415) hydrogen bonds : angle 6.08171 ( 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 389 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 335 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 TRP cc_start: 0.5936 (t-100) cc_final: 0.5245 (t-100) REVERT: A 300 GLN cc_start: 0.6222 (mt0) cc_final: 0.5868 (mm-40) REVERT: A 301 LYS cc_start: 0.6774 (mmtm) cc_final: 0.6535 (mmtm) REVERT: A 314 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6604 (mtp85) REVERT: B 25 MET cc_start: 0.7449 (tpt) cc_final: 0.7111 (tpt) REVERT: B 148 LEU cc_start: 0.7744 (mt) cc_final: 0.7190 (tp) REVERT: B 239 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7380 (mttt) REVERT: B 314 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7529 (tpt90) REVERT: C 42 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7939 (t) REVERT: C 58 LYS cc_start: 0.7007 (mttt) cc_final: 0.6807 (mttt) REVERT: C 94 ARG cc_start: 0.7079 (tpp80) cc_final: 0.6375 (mtt180) REVERT: C 239 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8013 (mtpp) REVERT: C 265 ARG cc_start: 0.6699 (ttp-110) cc_final: 0.6336 (mtt90) REVERT: C 314 ARG cc_start: 0.6670 (tmt170) cc_final: 0.6229 (tmt170) REVERT: D 148 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6170 (tp) REVERT: D 331 ILE cc_start: 0.6375 (OUTLIER) cc_final: 0.6111 (pt) REVERT: E 42 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (t) REVERT: E 125 TYR cc_start: 0.8116 (t80) cc_final: 0.7636 (t80) REVERT: E 176 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5073 (m-10) REVERT: F 46 GLU cc_start: 0.7069 (tt0) cc_final: 0.6703 (tt0) REVERT: F 67 LEU cc_start: 0.4026 (OUTLIER) cc_final: 0.3718 (pp) REVERT: F 105 THR cc_start: 0.5636 (p) cc_final: 0.5214 (t) REVERT: F 163 ASN cc_start: 0.8258 (m-40) cc_final: 0.7998 (m-40) REVERT: F 223 GLN cc_start: 0.5484 (mt0) cc_final: 0.5061 (mt0) REVERT: M 29 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.6988 (ptm160) REVERT: M 32 ASN cc_start: 0.7358 (m-40) cc_final: 0.6079 (p0) outliers start: 54 outliers final: 40 residues processed: 362 average time/residue: 0.1194 time to fit residues: 62.3262 Evaluate side-chains 371 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 325 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 233 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 176 PHE 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 42 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 90 THR 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 100 LEU 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 218 ARG 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 67 LEU Chi-restraints excluded: chain E residue 176 PHE 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 67 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 53 TRP Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 26 ILE 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: 7.9990 chunk 65 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 152 optimal weight: 0.0030 chunk 174 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 329 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN D 144 ASN E 140 HIS ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 ASN F 241 GLN F 322 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.206800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.180547 restraints weight = 19891.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179352 restraints weight = 19779.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181623 restraints weight = 15919.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183478 restraints weight = 11771.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183621 restraints weight = 10197.307| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 15710 Z= 0.277 Angle : 0.982 21.504 21627 Z= 0.494 Chirality : 0.049 0.324 2615 Planarity : 0.008 0.102 2759 Dihedral : 17.108 172.882 2770 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.44 % Allowed : 19.85 % Favored : 79.71 % Rotamer: Outliers : 4.13 % Allowed : 23.21 % Favored : 72.66 % 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 aren not related in a simple way. whole: -4.65 (0.16), residues: 2055 helix: -1.68 (0.23), residues: 470 sheet: -3.66 (0.21), residues: 379 loop : -3.64 (0.15), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 56 TYR 0.019 0.002 TYR B 125 PHE 0.046 0.003 PHE E 95 TRP 0.039 0.003 TRP B 270 HIS 0.011 0.002 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00636 (15710) covalent geometry : angle 0.98184 (21627) hydrogen bonds : bond 0.04038 ( 415) hydrogen bonds : angle 6.60622 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.70 seconds wall clock time: 39 minutes 2.90 seconds (2342.90 seconds total)