Starting phenix.real_space_refine on Fri Mar 6 07:18:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.map" model { file = "/net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rb0_24391/03_2026/7rb0_24391.cif" } resolution = 2.98 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16320 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10512 2.51 5 N 2652 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "E" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "F" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "A" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "B" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "C" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Time building chain proxies: 6.90, per 1000 atoms: 0.42 Number of scatterers: 16350 At special positions: 0 Unit cell: (108.861, 106.368, 125.481, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3120 8.00 N 2652 7.00 C 10512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 36 sheets defined 26.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.862A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'E' and resid 1 through 12 Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.854A pdb=" N ILE E 235 " --> pdb=" O ALA E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 259 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 1 through 12 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.603A pdb=" N ILE F 235 " --> pdb=" O ALA F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.805A pdb=" N ILE A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'B' and resid 1 through 12 Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.525A pdb=" N PHE B 203 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.647A pdb=" N ILE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.984A pdb=" N THR C 105 " --> pdb=" O CYS C 102 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP C 106 " --> pdb=" O SER C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 102 through 106' Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.507A pdb=" N ILE C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 298 through 309 Processing sheet with id=AA1, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.566A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 79 through 80 removed outlier: 6.967A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 266 removed outlier: 5.198A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.599A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.550A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.029A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AB2, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.886A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 281 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 315 through 322 removed outlier: 6.126A pdb=" N LYS E 334 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 25 through 26 removed outlier: 6.541A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.063A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AB7, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB8, first strand: chain 'F' and resid 264 through 266 removed outlier: 3.920A pdb=" N GLU F 264 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 281 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 322 removed outlier: 6.224A pdb=" N LYS F 334 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.551A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AC3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AC4, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.761A pdb=" N GLU A 264 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 281 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.545A pdb=" N LYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.543A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.067A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.784A pdb=" N GLU B 264 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 281 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.645A pdb=" N LYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.542A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AD6, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AD8, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.927A pdb=" N GLU C 264 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 281 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 315 through 322 removed outlier: 6.234A pdb=" N LYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.80 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: 5054 1.33 - 1.45: 2602 1.45 - 1.57: 8940 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16698 Sorted by residual: bond pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.41e-02 5.03e+03 1.10e+01 bond pdb=" CA LEU C 75 " pdb=" C LEU C 75 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.80e-02 3.09e+03 6.54e+00 bond pdb=" CA LEU F 75 " pdb=" C LEU F 75 " ideal model delta sigma weight residual 1.523 1.478 0.046 1.80e-02 3.09e+03 6.47e+00 bond pdb=" CB VAL D 24 " pdb=" CG2 VAL D 24 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB VAL E 24 " pdb=" CG2 VAL E 24 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 ... (remaining 16693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 22235 2.29 - 4.57: 424 4.57 - 6.86: 31 6.86 - 9.14: 0 9.14 - 11.43: 2 Bond angle restraints: 22692 Sorted by residual: angle pdb=" N TYR D 342 " pdb=" CA TYR D 342 " pdb=" C TYR D 342 " ideal model delta sigma weight residual 108.22 112.42 -4.20 9.00e-01 1.23e+00 2.18e+01 angle pdb=" CA LEU C 248 " pdb=" CB LEU C 248 " pdb=" CG LEU C 248 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA LEU F 248 " pdb=" CB LEU F 248 " pdb=" CG LEU F 248 " ideal model delta sigma weight residual 116.30 127.70 -11.40 3.50e+00 8.16e-02 1.06e+01 angle pdb=" N VAL C 101 " pdb=" CA VAL C 101 " pdb=" C VAL C 101 " ideal model delta sigma weight residual 111.48 108.58 2.90 9.40e-01 1.13e+00 9.50e+00 angle pdb=" CA TYR D 342 " pdb=" CB TYR D 342 " pdb=" CG TYR D 342 " ideal model delta sigma weight residual 113.90 119.41 -5.51 1.80e+00 3.09e-01 9.36e+00 ... (remaining 22687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 9073 17.05 - 34.09: 748 34.09 - 51.14: 98 51.14 - 68.18: 29 68.18 - 85.23: 18 Dihedral angle restraints: 9966 sinusoidal: 3900 harmonic: 6066 Sorted by residual: dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N LEU A 298 " pdb=" CA LEU A 298 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU C 297 " pdb=" C LEU C 297 " pdb=" N LEU C 298 " pdb=" CA LEU C 298 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU B 297 " pdb=" C LEU B 297 " pdb=" N LEU B 298 " pdb=" CA LEU B 298 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 9963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1566 0.044 - 0.088: 794 0.088 - 0.132: 230 0.132 - 0.176: 29 0.176 - 0.220: 3 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CG LEU F 248 " pdb=" CB LEU F 248 " pdb=" CD1 LEU F 248 " pdb=" CD2 LEU F 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU C 248 " pdb=" CB LEU C 248 " pdb=" CD1 LEU C 248 " pdb=" CD2 LEU C 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE D 252 " pdb=" CA ILE D 252 " pdb=" CG1 ILE D 252 " pdb=" CG2 ILE D 252 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 2619 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 134 " 0.009 2.00e-02 2.50e+03 1.50e-02 3.91e+00 pdb=" CG PHE E 134 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE E 134 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 134 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE E 134 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 134 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 134 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 179 " 0.015 2.00e-02 2.50e+03 1.29e-02 3.31e+00 pdb=" CG TYR A 179 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 179 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 179 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 179 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 134 " -0.012 2.00e-02 2.50e+03 1.36e-02 3.23e+00 pdb=" CG PHE A 134 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 134 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 134 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 134 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 134 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 134 " 0.000 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 408 2.67 - 3.23: 16567 3.23 - 3.79: 25738 3.79 - 4.34: 36575 4.34 - 4.90: 59373 Nonbonded interactions: 138661 Sorted by model distance: nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 225 " model vdw 2.115 3.040 nonbonded pdb=" OG1 THR F 98 " pdb=" OG1 THR F 105 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.142 3.040 nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.149 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" OH TYR B 225 " model vdw 2.152 3.040 ... (remaining 138656 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'B' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'C' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'D' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'E' and (resid -1 through 35 or resid 37 through 345)) selection = (chain 'F' and (resid -1 through 35 or resid 37 through 345)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.350 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 0.055 16698 Z= 0.407 Angle : 0.762 11.430 22692 Z= 0.422 Chirality : 0.052 0.220 2622 Planarity : 0.004 0.040 2922 Dihedral : 13.468 85.227 6054 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2076 helix: -1.13 (0.20), residues: 516 sheet: -0.81 (0.28), residues: 354 loop : -0.83 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 224 TYR 0.031 0.003 TYR A 179 PHE 0.033 0.003 PHE E 134 TRP 0.026 0.003 TRP D 332 HIS 0.006 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00944 (16698) covalent geometry : angle 0.76173 (22692) hydrogen bonds : bond 0.15329 ( 565) hydrogen bonds : angle 8.32552 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: D 220 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6904 (tp30) REVERT: E 91 ASP cc_start: 0.8023 (t0) cc_final: 0.7644 (t0) REVERT: E 193 TYR cc_start: 0.8289 (m-80) cc_final: 0.8023 (m-80) REVERT: F 91 ASP cc_start: 0.7919 (t0) cc_final: 0.7532 (t0) REVERT: B 193 TYR cc_start: 0.7858 (m-10) cc_final: 0.7632 (m-10) REVERT: C 193 TYR cc_start: 0.8285 (m-80) cc_final: 0.8063 (m-80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5336 time to fit residues: 185.1378 Evaluate side-chains 239 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 ASN E 82 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 242 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107643 restraints weight = 44485.636| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.04 r_work: 0.3140 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16698 Z= 0.146 Angle : 0.605 10.221 22692 Z= 0.320 Chirality : 0.047 0.183 2622 Planarity : 0.004 0.045 2922 Dihedral : 5.094 21.346 2208 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.48 % Allowed : 11.35 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.18), residues: 2076 helix: -0.31 (0.22), residues: 528 sheet: -0.40 (0.29), residues: 354 loop : -0.80 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 138 TYR 0.020 0.002 TYR E 342 PHE 0.014 0.002 PHE B 134 TRP 0.017 0.002 TRP D 332 HIS 0.004 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00332 (16698) covalent geometry : angle 0.60464 (22692) hydrogen bonds : bond 0.04002 ( 565) hydrogen bonds : angle 6.05518 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 316 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 199 ASN cc_start: 0.8379 (t0) cc_final: 0.8047 (t0) REVERT: D 342 TYR cc_start: 0.2517 (p90) cc_final: 0.2182 (p90) REVERT: E 91 ASP cc_start: 0.8657 (t0) cc_final: 0.8340 (t0) REVERT: E 193 TYR cc_start: 0.8699 (m-80) cc_final: 0.8334 (m-80) REVERT: E 257 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7481 (tmm160) REVERT: E 301 ASP cc_start: 0.8539 (m-30) cc_final: 0.8334 (m-30) REVERT: F 91 ASP cc_start: 0.8664 (t0) cc_final: 0.8293 (t0) REVERT: F 138 ARG cc_start: 0.8135 (tpm-80) cc_final: 0.7891 (tpm-80) REVERT: F 179 TYR cc_start: 0.8301 (m-80) cc_final: 0.8078 (m-80) REVERT: F 193 TYR cc_start: 0.8635 (m-80) cc_final: 0.8055 (m-80) REVERT: F 257 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7384 (tmm160) REVERT: F 301 ASP cc_start: 0.8511 (m-30) cc_final: 0.8233 (m-30) REVERT: B 179 TYR cc_start: 0.8388 (m-80) cc_final: 0.8169 (m-80) REVERT: B 193 TYR cc_start: 0.8206 (m-10) cc_final: 0.7735 (m-10) REVERT: B 329 PHE cc_start: 0.8381 (m-80) cc_final: 0.8030 (m-80) REVERT: C 193 TYR cc_start: 0.8565 (m-80) cc_final: 0.8267 (m-80) REVERT: C 257 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7386 (tmm160) REVERT: C 342 TYR cc_start: 0.2631 (p90) cc_final: 0.2276 (p90) outliers start: 27 outliers final: 9 residues processed: 326 average time/residue: 0.4974 time to fit residues: 182.6736 Evaluate side-chains 282 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 40 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 129 optimal weight: 0.0030 chunk 14 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 163 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN C 163 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.172885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112963 restraints weight = 38538.521| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.82 r_work: 0.3222 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16698 Z= 0.105 Angle : 0.554 8.579 22692 Z= 0.291 Chirality : 0.045 0.176 2622 Planarity : 0.004 0.049 2922 Dihedral : 4.644 18.595 2208 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 13.71 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2076 helix: 0.02 (0.23), residues: 528 sheet: -0.07 (0.29), residues: 354 loop : -0.73 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 138 TYR 0.016 0.001 TYR D 342 PHE 0.015 0.002 PHE E 134 TRP 0.016 0.001 TRP D 332 HIS 0.004 0.001 HIS E 337 Details of bonding type rmsd covalent geometry : bond 0.00232 (16698) covalent geometry : angle 0.55399 (22692) hydrogen bonds : bond 0.03309 ( 565) hydrogen bonds : angle 5.52888 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: D 199 ASN cc_start: 0.8379 (t0) cc_final: 0.8050 (t0) REVERT: E 91 ASP cc_start: 0.8442 (t0) cc_final: 0.8149 (t0) REVERT: E 193 TYR cc_start: 0.8734 (m-80) cc_final: 0.8033 (m-10) REVERT: E 221 PHE cc_start: 0.5198 (t80) cc_final: 0.4783 (t80) REVERT: F 91 ASP cc_start: 0.8580 (t0) cc_final: 0.8234 (t0) REVERT: F 138 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (tpm-80) REVERT: F 193 TYR cc_start: 0.8661 (m-80) cc_final: 0.7977 (m-80) REVERT: F 201 GLN cc_start: 0.8720 (mp10) cc_final: 0.8091 (pm20) REVERT: F 221 PHE cc_start: 0.5300 (t80) cc_final: 0.4924 (t80) REVERT: F 301 ASP cc_start: 0.8392 (m-30) cc_final: 0.8074 (m-30) REVERT: F 329 PHE cc_start: 0.8140 (m-80) cc_final: 0.7386 (m-80) REVERT: A 138 ARG cc_start: 0.8467 (tmt-80) cc_final: 0.8155 (tmt-80) REVERT: A 221 PHE cc_start: 0.5209 (t80) cc_final: 0.4776 (t80) REVERT: B 201 GLN cc_start: 0.8746 (mp10) cc_final: 0.8227 (pm20) REVERT: B 221 PHE cc_start: 0.5115 (t80) cc_final: 0.4671 (t80) REVERT: B 329 PHE cc_start: 0.8090 (m-80) cc_final: 0.7557 (m-80) REVERT: B 342 TYR cc_start: 0.2749 (p90) cc_final: 0.2451 (p90) REVERT: C 138 ARG cc_start: 0.7933 (tpm-80) cc_final: 0.7533 (tpm-80) REVERT: C 193 TYR cc_start: 0.8453 (m-80) cc_final: 0.7992 (m-80) REVERT: C 201 GLN cc_start: 0.8712 (mp10) cc_final: 0.8084 (pm20) REVERT: C 329 PHE cc_start: 0.8157 (m-80) cc_final: 0.7359 (m-80) REVERT: C 342 TYR cc_start: 0.2952 (p90) cc_final: 0.2718 (p90) outliers start: 35 outliers final: 9 residues processed: 368 average time/residue: 0.4818 time to fit residues: 200.7896 Evaluate side-chains 317 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 152 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 114 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 4 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 189 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 152 GLN D 277 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS B 309 GLN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 277 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112763 restraints weight = 40598.156| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.92 r_work: 0.3230 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16698 Z= 0.104 Angle : 0.573 9.094 22692 Z= 0.298 Chirality : 0.045 0.199 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.467 15.840 2208 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.75 % Allowed : 16.67 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2076 helix: 0.23 (0.23), residues: 528 sheet: 0.19 (0.28), residues: 354 loop : -0.65 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.013 0.001 TYR C 342 PHE 0.025 0.001 PHE A 134 TRP 0.015 0.001 TRP D 332 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00233 (16698) covalent geometry : angle 0.57341 (22692) hydrogen bonds : bond 0.03092 ( 565) hydrogen bonds : angle 5.32175 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: D 68 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: D 199 ASN cc_start: 0.8361 (t0) cc_final: 0.7564 (t0) REVERT: D 201 GLN cc_start: 0.8879 (mp10) cc_final: 0.8614 (mp10) REVERT: E 91 ASP cc_start: 0.8462 (t0) cc_final: 0.8153 (t0) REVERT: E 193 TYR cc_start: 0.8749 (m-80) cc_final: 0.8070 (m-10) REVERT: E 221 PHE cc_start: 0.5140 (t80) cc_final: 0.4800 (t80) REVERT: E 257 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7202 (tmm160) REVERT: F 91 ASP cc_start: 0.8607 (t0) cc_final: 0.8242 (t0) REVERT: F 104 MET cc_start: 0.5009 (pmm) cc_final: 0.4764 (pmm) REVERT: F 179 TYR cc_start: 0.8273 (m-80) cc_final: 0.7943 (m-80) REVERT: F 193 TYR cc_start: 0.8650 (m-80) cc_final: 0.8042 (m-80) REVERT: F 201 GLN cc_start: 0.8691 (mp10) cc_final: 0.8086 (pm20) REVERT: F 221 PHE cc_start: 0.5208 (t80) cc_final: 0.4875 (t80) REVERT: F 257 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7650 (tmm160) REVERT: F 301 ASP cc_start: 0.8343 (m-30) cc_final: 0.8022 (m-30) REVERT: F 329 PHE cc_start: 0.8106 (m-80) cc_final: 0.7487 (m-80) REVERT: A 102 CYS cc_start: 0.4081 (OUTLIER) cc_final: 0.3831 (t) REVERT: A 221 PHE cc_start: 0.5197 (t80) cc_final: 0.4792 (t80) REVERT: A 235 ILE cc_start: 0.8010 (pt) cc_final: 0.7734 (pp) REVERT: B 201 GLN cc_start: 0.8710 (mp10) cc_final: 0.8246 (pm20) REVERT: B 221 PHE cc_start: 0.5165 (t80) cc_final: 0.4723 (t80) REVERT: B 329 PHE cc_start: 0.8002 (m-80) cc_final: 0.7537 (m-80) REVERT: B 342 TYR cc_start: 0.2670 (p90) cc_final: 0.2377 (p90) REVERT: C 138 ARG cc_start: 0.7819 (tpm-80) cc_final: 0.7453 (tpm-80) REVERT: C 179 TYR cc_start: 0.8227 (m-80) cc_final: 0.7742 (m-80) REVERT: C 193 TYR cc_start: 0.8426 (m-80) cc_final: 0.8054 (m-80) REVERT: C 201 GLN cc_start: 0.8646 (mp10) cc_final: 0.8045 (pm20) REVERT: C 272 ASP cc_start: 0.8860 (t0) cc_final: 0.8645 (t70) REVERT: C 329 PHE cc_start: 0.8119 (m-80) cc_final: 0.7480 (m-80) REVERT: C 342 TYR cc_start: 0.2795 (p90) cc_final: 0.2569 (p90) outliers start: 32 outliers final: 13 residues processed: 354 average time/residue: 0.5277 time to fit residues: 209.3964 Evaluate side-chains 314 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 297 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 1.9990 chunk 168 optimal weight: 0.0770 chunk 135 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN D 19 GLN D 28 ASN D 242 HIS E 18 GLN E 28 ASN E 152 GLN E 163 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.170207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109382 restraints weight = 34161.747| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.60 r_work: 0.3175 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16698 Z= 0.187 Angle : 0.617 9.358 22692 Z= 0.323 Chirality : 0.047 0.196 2622 Planarity : 0.004 0.051 2922 Dihedral : 4.578 14.960 2208 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.47 % Allowed : 17.98 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2076 helix: 0.22 (0.23), residues: 534 sheet: 0.26 (0.28), residues: 354 loop : -0.60 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 224 TYR 0.020 0.001 TYR C 342 PHE 0.033 0.002 PHE E 194 TRP 0.017 0.001 TRP D 332 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00444 (16698) covalent geometry : angle 0.61675 (22692) hydrogen bonds : bond 0.03591 ( 565) hydrogen bonds : angle 5.49378 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.603 Fit side-chains REVERT: D 68 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: D 199 ASN cc_start: 0.8433 (t0) cc_final: 0.7634 (t0) REVERT: D 201 GLN cc_start: 0.8851 (mp10) cc_final: 0.8532 (mp10) REVERT: E 91 ASP cc_start: 0.8437 (t0) cc_final: 0.8078 (t0) REVERT: E 193 TYR cc_start: 0.8721 (m-80) cc_final: 0.8350 (m-80) REVERT: E 221 PHE cc_start: 0.5218 (t80) cc_final: 0.4868 (t80) REVERT: E 257 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7305 (tmm160) REVERT: E 301 ASP cc_start: 0.8395 (m-30) cc_final: 0.8093 (m-30) REVERT: F 91 ASP cc_start: 0.8614 (t0) cc_final: 0.8228 (t0) REVERT: F 104 MET cc_start: 0.4939 (pmm) cc_final: 0.4657 (pmm) REVERT: F 179 TYR cc_start: 0.8396 (m-80) cc_final: 0.8195 (m-80) REVERT: F 193 TYR cc_start: 0.8610 (m-80) cc_final: 0.7984 (m-80) REVERT: F 201 GLN cc_start: 0.8626 (mp10) cc_final: 0.8094 (pm20) REVERT: F 221 PHE cc_start: 0.5273 (t80) cc_final: 0.4920 (t80) REVERT: F 257 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7192 (tmm160) REVERT: F 301 ASP cc_start: 0.8396 (m-30) cc_final: 0.8096 (m-30) REVERT: F 329 PHE cc_start: 0.8125 (m-80) cc_final: 0.7405 (m-80) REVERT: A 138 ARG cc_start: 0.8149 (tmt-80) cc_final: 0.7746 (tmt-80) REVERT: A 221 PHE cc_start: 0.5240 (t80) cc_final: 0.4859 (t80) REVERT: A 257 ARG cc_start: 0.8265 (tpp-160) cc_final: 0.7941 (tpm170) REVERT: B 201 GLN cc_start: 0.8731 (mp10) cc_final: 0.8316 (pm20) REVERT: B 221 PHE cc_start: 0.5198 (t80) cc_final: 0.4735 (t80) REVERT: C 179 TYR cc_start: 0.8339 (m-80) cc_final: 0.8114 (m-80) REVERT: C 193 TYR cc_start: 0.8416 (m-80) cc_final: 0.8012 (m-80) REVERT: C 201 GLN cc_start: 0.8606 (mp10) cc_final: 0.8072 (pm20) REVERT: C 272 ASP cc_start: 0.8786 (t0) cc_final: 0.8549 (t70) REVERT: C 329 PHE cc_start: 0.8209 (m-80) cc_final: 0.7374 (m-80) outliers start: 45 outliers final: 18 residues processed: 327 average time/residue: 0.5076 time to fit residues: 187.0015 Evaluate side-chains 305 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 242 HIS E 18 GLN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112501 restraints weight = 31665.082| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.39 r_work: 0.3213 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16698 Z= 0.174 Angle : 0.613 11.787 22692 Z= 0.319 Chirality : 0.047 0.265 2622 Planarity : 0.004 0.051 2922 Dihedral : 4.619 14.847 2208 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.47 % Allowed : 18.31 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2076 helix: 0.14 (0.23), residues: 534 sheet: 0.31 (0.28), residues: 354 loop : -0.59 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 224 TYR 0.011 0.001 TYR F 342 PHE 0.026 0.002 PHE E 194 TRP 0.020 0.001 TRP D 332 HIS 0.003 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00410 (16698) covalent geometry : angle 0.61334 (22692) hydrogen bonds : bond 0.03589 ( 565) hydrogen bonds : angle 5.51809 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 293 time to evaluate : 0.516 Fit side-chains REVERT: D 68 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: D 138 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7659 (tmt-80) REVERT: D 199 ASN cc_start: 0.8460 (t0) cc_final: 0.7546 (t0) REVERT: D 201 GLN cc_start: 0.8766 (mp10) cc_final: 0.8373 (mp10) REVERT: E 193 TYR cc_start: 0.8725 (m-80) cc_final: 0.8394 (m-80) REVERT: E 221 PHE cc_start: 0.5271 (t80) cc_final: 0.4863 (t80) REVERT: E 257 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7309 (tmm160) REVERT: F 91 ASP cc_start: 0.8559 (t0) cc_final: 0.8167 (t0) REVERT: F 104 MET cc_start: 0.4965 (pmm) cc_final: 0.4704 (pmm) REVERT: F 138 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7818 (tpm-80) REVERT: F 193 TYR cc_start: 0.8583 (m-80) cc_final: 0.8010 (m-80) REVERT: F 201 GLN cc_start: 0.8625 (mp10) cc_final: 0.8127 (pm20) REVERT: F 221 PHE cc_start: 0.5239 (t80) cc_final: 0.4871 (t80) REVERT: F 257 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7190 (tmm160) REVERT: F 301 ASP cc_start: 0.8418 (m-30) cc_final: 0.8137 (m-30) REVERT: F 329 PHE cc_start: 0.8133 (m-80) cc_final: 0.7367 (m-80) REVERT: A 193 TYR cc_start: 0.7937 (m-10) cc_final: 0.7729 (m-10) REVERT: A 201 GLN cc_start: 0.8757 (mp10) cc_final: 0.8322 (pm20) REVERT: A 221 PHE cc_start: 0.5438 (t80) cc_final: 0.5041 (t80) REVERT: B 201 GLN cc_start: 0.8692 (mp10) cc_final: 0.8341 (pm20) REVERT: B 221 PHE cc_start: 0.5213 (t80) cc_final: 0.4821 (t80) REVERT: C 102 CYS cc_start: 0.3732 (OUTLIER) cc_final: 0.2980 (t) REVERT: C 193 TYR cc_start: 0.8431 (m-80) cc_final: 0.8038 (m-80) REVERT: C 201 GLN cc_start: 0.8610 (mp10) cc_final: 0.8108 (pm20) REVERT: C 257 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7130 (tmm160) REVERT: C 272 ASP cc_start: 0.8752 (t0) cc_final: 0.8545 (t70) REVERT: C 329 PHE cc_start: 0.8201 (m-80) cc_final: 0.7517 (m-80) outliers start: 45 outliers final: 20 residues processed: 315 average time/residue: 0.4947 time to fit residues: 175.7702 Evaluate side-chains 313 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 138 ARG Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 195 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.172730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110529 restraints weight = 54564.972| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.51 r_work: 0.3172 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16698 Z= 0.131 Angle : 0.602 10.129 22692 Z= 0.311 Chirality : 0.046 0.185 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.498 15.033 2208 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.36 % Allowed : 19.46 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.18), residues: 2076 helix: 0.21 (0.24), residues: 534 sheet: 0.42 (0.29), residues: 354 loop : -0.55 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 224 TYR 0.011 0.001 TYR F 342 PHE 0.022 0.002 PHE E 134 TRP 0.021 0.001 TRP D 332 HIS 0.003 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00306 (16698) covalent geometry : angle 0.60242 (22692) hydrogen bonds : bond 0.03347 ( 565) hydrogen bonds : angle 5.38378 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 0.597 Fit side-chains REVERT: D 68 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: D 138 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7620 (tmt-80) REVERT: D 179 TYR cc_start: 0.8453 (m-80) cc_final: 0.8230 (m-80) REVERT: D 199 ASN cc_start: 0.8453 (t0) cc_final: 0.7634 (t0) REVERT: D 201 GLN cc_start: 0.8828 (mp10) cc_final: 0.8392 (mp10) REVERT: D 284 GLN cc_start: 0.8234 (mt0) cc_final: 0.7861 (tp40) REVERT: E 193 TYR cc_start: 0.8751 (m-80) cc_final: 0.8397 (m-80) REVERT: E 221 PHE cc_start: 0.5275 (t80) cc_final: 0.4883 (t80) REVERT: E 257 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7344 (tmm160) REVERT: F 104 MET cc_start: 0.4909 (pmm) cc_final: 0.4672 (pmm) REVERT: F 193 TYR cc_start: 0.8629 (m-80) cc_final: 0.8062 (m-80) REVERT: F 201 GLN cc_start: 0.8683 (mp10) cc_final: 0.8162 (pm20) REVERT: F 221 PHE cc_start: 0.5206 (t80) cc_final: 0.4889 (t80) REVERT: F 257 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7657 (tmm160) REVERT: F 301 ASP cc_start: 0.8281 (m-30) cc_final: 0.7995 (m-30) REVERT: F 329 PHE cc_start: 0.8143 (m-80) cc_final: 0.7418 (m-80) REVERT: A 201 GLN cc_start: 0.8751 (mp10) cc_final: 0.8420 (pm20) REVERT: B 179 TYR cc_start: 0.8358 (m-80) cc_final: 0.8139 (m-80) REVERT: B 201 GLN cc_start: 0.8652 (mp10) cc_final: 0.8275 (pm20) REVERT: B 221 PHE cc_start: 0.5232 (t80) cc_final: 0.4870 (t80) REVERT: C 102 CYS cc_start: 0.3709 (OUTLIER) cc_final: 0.2928 (t) REVERT: C 179 TYR cc_start: 0.8351 (m-80) cc_final: 0.8104 (m-80) REVERT: C 193 TYR cc_start: 0.8456 (m-80) cc_final: 0.8086 (m-80) REVERT: C 201 GLN cc_start: 0.8678 (mp10) cc_final: 0.8139 (pm20) REVERT: C 257 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7149 (tmm160) REVERT: C 329 PHE cc_start: 0.8225 (m-80) cc_final: 0.7406 (m-80) outliers start: 43 outliers final: 21 residues processed: 327 average time/residue: 0.4738 time to fit residues: 175.6339 Evaluate side-chains 312 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 319 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 162 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 277 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109239 restraints weight = 44553.086| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.09 r_work: 0.3165 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16698 Z= 0.144 Angle : 0.610 10.671 22692 Z= 0.315 Chirality : 0.046 0.178 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.515 16.638 2208 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2076 helix: 0.21 (0.23), residues: 534 sheet: 0.47 (0.29), residues: 354 loop : -0.55 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 138 TYR 0.013 0.001 TYR A 342 PHE 0.030 0.002 PHE F 194 TRP 0.023 0.001 TRP D 332 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00337 (16698) covalent geometry : angle 0.61039 (22692) hydrogen bonds : bond 0.03486 ( 565) hydrogen bonds : angle 5.44305 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 0.758 Fit side-chains REVERT: D 68 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: D 199 ASN cc_start: 0.8448 (t0) cc_final: 0.7619 (t0) REVERT: D 201 GLN cc_start: 0.8836 (mp10) cc_final: 0.8367 (mp10) REVERT: D 284 GLN cc_start: 0.8214 (mt0) cc_final: 0.7838 (tp40) REVERT: E 193 TYR cc_start: 0.8744 (m-80) cc_final: 0.8418 (m-80) REVERT: E 221 PHE cc_start: 0.5196 (t80) cc_final: 0.4839 (t80) REVERT: E 257 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7327 (tmm160) REVERT: F 104 MET cc_start: 0.4949 (pmm) cc_final: 0.4723 (pmm) REVERT: F 193 TYR cc_start: 0.8520 (m-80) cc_final: 0.8008 (m-80) REVERT: F 201 GLN cc_start: 0.8663 (mp10) cc_final: 0.8140 (pm20) REVERT: F 221 PHE cc_start: 0.5255 (t80) cc_final: 0.4955 (t80) REVERT: F 257 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7663 (tmm160) REVERT: F 301 ASP cc_start: 0.8270 (m-30) cc_final: 0.7985 (m-30) REVERT: F 307 LYS cc_start: 0.7784 (mttt) cc_final: 0.7442 (mmtt) REVERT: F 329 PHE cc_start: 0.8174 (m-80) cc_final: 0.7406 (m-80) REVERT: A 138 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7642 (tmt-80) REVERT: A 179 TYR cc_start: 0.8420 (m-80) cc_final: 0.8159 (m-80) REVERT: A 201 GLN cc_start: 0.8734 (mp10) cc_final: 0.8430 (pm20) REVERT: B 193 TYR cc_start: 0.8128 (m-10) cc_final: 0.7597 (m-10) REVERT: B 201 GLN cc_start: 0.8639 (mp10) cc_final: 0.8262 (pm20) REVERT: B 221 PHE cc_start: 0.5132 (t80) cc_final: 0.4778 (t80) REVERT: B 257 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.8072 (tpp-160) REVERT: B 301 ASP cc_start: 0.8332 (m-30) cc_final: 0.8080 (m-30) REVERT: C 102 CYS cc_start: 0.3870 (OUTLIER) cc_final: 0.3199 (t) REVERT: C 193 TYR cc_start: 0.8438 (m-80) cc_final: 0.7980 (m-80) REVERT: C 201 GLN cc_start: 0.8631 (mp10) cc_final: 0.8100 (pm20) REVERT: C 257 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7141 (tmm160) REVERT: C 329 PHE cc_start: 0.8224 (m-80) cc_final: 0.7385 (m-80) outliers start: 41 outliers final: 26 residues processed: 311 average time/residue: 0.4919 time to fit residues: 173.5049 Evaluate side-chains 315 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain F residue 333 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 78 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 148 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN A 28 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS A 277 ASN B 28 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.172269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110278 restraints weight = 44646.476| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.12 r_work: 0.3175 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16698 Z= 0.154 Angle : 0.624 10.907 22692 Z= 0.321 Chirality : 0.046 0.188 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.533 15.938 2208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.30 % Allowed : 20.50 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 2076 helix: 0.19 (0.23), residues: 534 sheet: 0.18 (0.29), residues: 360 loop : -0.41 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 138 TYR 0.014 0.002 TYR B 342 PHE 0.029 0.002 PHE F 194 TRP 0.022 0.001 TRP D 332 HIS 0.008 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00362 (16698) covalent geometry : angle 0.62397 (22692) hydrogen bonds : bond 0.03563 ( 565) hydrogen bonds : angle 5.47704 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.648 Fit side-chains REVERT: D 68 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: D 138 ARG cc_start: 0.8089 (tmt-80) cc_final: 0.7835 (tmt-80) REVERT: D 199 ASN cc_start: 0.8475 (t0) cc_final: 0.8083 (t0) REVERT: D 284 GLN cc_start: 0.8247 (mt0) cc_final: 0.7869 (tp40) REVERT: E 193 TYR cc_start: 0.8755 (m-80) cc_final: 0.8404 (m-80) REVERT: E 221 PHE cc_start: 0.5175 (t80) cc_final: 0.4836 (t80) REVERT: E 257 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7387 (tmm160) REVERT: F 104 MET cc_start: 0.4966 (pmm) cc_final: 0.4731 (pmm) REVERT: F 193 TYR cc_start: 0.8558 (m-80) cc_final: 0.8013 (m-80) REVERT: F 201 GLN cc_start: 0.8661 (mp10) cc_final: 0.8143 (pm20) REVERT: F 221 PHE cc_start: 0.5250 (t80) cc_final: 0.4992 (t80) REVERT: F 257 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7706 (tmm160) REVERT: F 301 ASP cc_start: 0.8275 (m-30) cc_final: 0.7976 (m-30) REVERT: F 307 LYS cc_start: 0.7781 (mttt) cc_final: 0.7447 (mmtt) REVERT: F 329 PHE cc_start: 0.8222 (m-80) cc_final: 0.7378 (m-80) REVERT: A 138 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7660 (tmt-80) REVERT: A 179 TYR cc_start: 0.8427 (m-80) cc_final: 0.8193 (m-80) REVERT: A 201 GLN cc_start: 0.8717 (mp10) cc_final: 0.8442 (pm20) REVERT: B 193 TYR cc_start: 0.8133 (m-10) cc_final: 0.7587 (m-10) REVERT: B 201 GLN cc_start: 0.8663 (mp10) cc_final: 0.8270 (pm20) REVERT: B 221 PHE cc_start: 0.5125 (t80) cc_final: 0.4793 (t80) REVERT: B 301 ASP cc_start: 0.8336 (m-30) cc_final: 0.8046 (m-30) REVERT: C 102 CYS cc_start: 0.4049 (OUTLIER) cc_final: 0.3746 (t) REVERT: C 193 TYR cc_start: 0.8422 (m-80) cc_final: 0.7962 (m-80) REVERT: C 201 GLN cc_start: 0.8661 (mp10) cc_final: 0.8130 (pm20) REVERT: C 257 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7117 (tmm160) REVERT: C 329 PHE cc_start: 0.8253 (m-80) cc_final: 0.7330 (m-80) outliers start: 42 outliers final: 28 residues processed: 310 average time/residue: 0.4809 time to fit residues: 169.4801 Evaluate side-chains 309 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain F residue 333 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 17 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 112 optimal weight: 0.0270 chunk 68 optimal weight: 8.9990 chunk 14 optimal weight: 0.0050 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117640 restraints weight = 54781.299| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.48 r_work: 0.3192 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16698 Z= 0.105 Angle : 0.614 11.420 22692 Z= 0.315 Chirality : 0.046 0.188 2622 Planarity : 0.004 0.054 2922 Dihedral : 4.362 16.692 2208 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.81 % Allowed : 20.89 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 2076 helix: 0.22 (0.24), residues: 534 sheet: 0.30 (0.29), residues: 360 loop : -0.34 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 138 TYR 0.014 0.001 TYR B 342 PHE 0.021 0.001 PHE E 134 TRP 0.021 0.001 TRP D 332 HIS 0.023 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00234 (16698) covalent geometry : angle 0.61397 (22692) hydrogen bonds : bond 0.03194 ( 565) hydrogen bonds : angle 5.30088 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 314 time to evaluate : 0.613 Fit side-chains REVERT: D 68 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: D 199 ASN cc_start: 0.8286 (t0) cc_final: 0.7765 (t0) REVERT: D 284 GLN cc_start: 0.8211 (mt0) cc_final: 0.7830 (tp40) REVERT: D 307 LYS cc_start: 0.7664 (mttt) cc_final: 0.7160 (mmtt) REVERT: E 193 TYR cc_start: 0.8719 (m-80) cc_final: 0.8397 (m-80) REVERT: E 221 PHE cc_start: 0.5036 (t80) cc_final: 0.4821 (t80) REVERT: E 257 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7394 (tmm160) REVERT: E 301 ASP cc_start: 0.8394 (m-30) cc_final: 0.8019 (m-30) REVERT: F 193 TYR cc_start: 0.8510 (m-80) cc_final: 0.7921 (m-80) REVERT: F 201 GLN cc_start: 0.8663 (mp10) cc_final: 0.8124 (pm20) REVERT: F 206 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8464 (mtt180) REVERT: F 257 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7784 (tmm160) REVERT: F 301 ASP cc_start: 0.8263 (m-30) cc_final: 0.7943 (m-30) REVERT: F 307 LYS cc_start: 0.7722 (mttt) cc_final: 0.7365 (mmtt) REVERT: F 329 PHE cc_start: 0.7966 (m-80) cc_final: 0.7351 (m-80) REVERT: A 201 GLN cc_start: 0.8665 (mp10) cc_final: 0.8381 (pm20) REVERT: A 221 PHE cc_start: 0.5328 (t80) cc_final: 0.5011 (t80) REVERT: B 179 TYR cc_start: 0.8345 (m-80) cc_final: 0.8111 (m-80) REVERT: B 201 GLN cc_start: 0.8595 (mp10) cc_final: 0.8161 (pm20) REVERT: B 221 PHE cc_start: 0.5150 (t80) cc_final: 0.4859 (t80) REVERT: C 102 CYS cc_start: 0.3950 (OUTLIER) cc_final: 0.3741 (t) REVERT: C 159 GLN cc_start: 0.8855 (pm20) cc_final: 0.8491 (pm20) REVERT: C 193 TYR cc_start: 0.8374 (m-80) cc_final: 0.7931 (m-10) REVERT: C 201 GLN cc_start: 0.8627 (mp10) cc_final: 0.8062 (pm20) REVERT: C 307 LYS cc_start: 0.7681 (mttt) cc_final: 0.7238 (mmtt) REVERT: C 329 PHE cc_start: 0.8006 (m-80) cc_final: 0.7330 (m-80) outliers start: 33 outliers final: 17 residues processed: 328 average time/residue: 0.4956 time to fit residues: 184.0906 Evaluate side-chains 311 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 257 ARG Chi-restraints excluded: chain F residue 242 HIS Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 333 CYS Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0170 chunk 29 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 147 optimal weight: 0.0870 chunk 184 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN E 18 GLN E 28 ASN ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 28 ASN ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 28 ASN ** C 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110726 restraints weight = 39292.504| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.79 r_work: 0.3192 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16698 Z= 0.147 Angle : 0.630 11.828 22692 Z= 0.324 Chirality : 0.046 0.180 2622 Planarity : 0.004 0.052 2922 Dihedral : 4.431 18.151 2208 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.43 % Allowed : 21.93 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 2076 helix: 0.26 (0.24), residues: 534 sheet: 0.61 (0.29), residues: 354 loop : -0.49 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 257 TYR 0.017 0.001 TYR A 342 PHE 0.029 0.002 PHE F 194 TRP 0.022 0.001 TRP D 332 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00351 (16698) covalent geometry : angle 0.63028 (22692) hydrogen bonds : bond 0.03471 ( 565) hydrogen bonds : angle 5.35717 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6585.41 seconds wall clock time: 112 minutes 48.13 seconds (6768.13 seconds total)