Starting phenix.real_space_refine on Sun Oct 25 08:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.map" model { file = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n33_24137/10_2026/7n33_24137.cif" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= 0.039 sd= 0.161 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 66 5.16 5 C 10596 2.51 5 N 2676 2.21 5 O 3174 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16524 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 3.42, per 1000 atoms: 0.21 Number of scatterers: 16524 At special positions: 0 Unit cell: (107.555, 107.963, 123.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 6 15.00 F 6 9.00 O 3174 8.00 N 2676 7.00 C 10596 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: 1.15 Conformation dependent library (CDL) restraints added in 588.6 milliseconds 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 26.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 226 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.582A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.152A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 7.152A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 7.910A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.962A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 7.302A pdb=" N SER A 329 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET A 331 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 342 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP A 333 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.582A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 7.910A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 4.962A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 323 removed outlier: 7.303A pdb=" N SER B 329 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET B 331 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE B 342 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP B 333 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.582A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.910A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.961A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 316 through 323 removed outlier: 7.303A pdb=" N SER C 329 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET C 331 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 342 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP C 333 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.582A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.152A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 7.152A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 7.910A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.962A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 removed outlier: 7.304A pdb=" N SER D 329 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET D 331 " --> pdb=" O PHE D 342 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE D 342 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP D 333 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.581A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 7.910A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 267 removed outlier: 4.962A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 323 removed outlier: 7.303A pdb=" N SER E 329 " --> pdb=" O PRO E 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET E 331 " --> pdb=" O PHE E 342 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE E 342 " --> pdb=" O MET E 331 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP E 333 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.582A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 7.151A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 7.911A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 4.962A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 7.303A pdb=" N SER F 329 " --> pdb=" O PRO F 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET F 331 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE F 342 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP F 333 " --> pdb=" O GLU F 340 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1746 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: 2.72 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5239 1.33 - 1.45: 2266 1.45 - 1.57: 9253 1.57 - 1.69: 12 1.69 - 1.81: 102 Bond restraints: 16872 Sorted by residual: bond pdb=" C3' UFT L 401 " pdb=" O3' UFT L 401 " ideal model delta sigma weight residual 1.378 1.432 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" C3' UFT J 401 " pdb=" O3' UFT J 401 " ideal model delta sigma weight residual 1.378 1.431 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C3' UFT I 401 " pdb=" O3' UFT I 401 " ideal model delta sigma weight residual 1.378 1.431 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C3' UFT H 401 " pdb=" O3' UFT H 401 " ideal model delta sigma weight residual 1.378 1.431 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C3' UFT K 401 " pdb=" O3' UFT K 401 " ideal model delta sigma weight residual 1.378 1.430 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 16867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 21732 1.12 - 2.24: 854 2.24 - 3.36: 256 3.36 - 4.48: 36 4.48 - 5.59: 24 Bond angle restraints: 22902 Sorted by residual: angle pdb=" C3' UFT I 401 " pdb=" O3' UFT I 401 " pdb=" P A I 402 " ideal model delta sigma weight residual 119.70 122.41 -2.71 1.20e+00 6.94e-01 5.11e+00 angle pdb=" C3' UFT H 401 " pdb=" O3' UFT H 401 " pdb=" P A H 402 " ideal model delta sigma weight residual 119.70 122.41 -2.71 1.20e+00 6.94e-01 5.08e+00 angle pdb=" C PHE F 342 " pdb=" N TYR F 343 " pdb=" CA TYR F 343 " ideal model delta sigma weight residual 122.90 118.24 4.66 2.07e+00 2.33e-01 5.08e+00 angle pdb=" C PHE C 342 " pdb=" N TYR C 343 " pdb=" CA TYR C 343 " ideal model delta sigma weight residual 122.90 118.24 4.66 2.07e+00 2.33e-01 5.06e+00 angle pdb=" C PHE E 342 " pdb=" N TYR E 343 " pdb=" CA TYR E 343 " ideal model delta sigma weight residual 122.90 118.25 4.65 2.07e+00 2.33e-01 5.06e+00 ... (remaining 22897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.43: 9924 29.43 - 58.86: 204 58.86 - 88.29: 30 88.29 - 117.72: 6 117.72 - 147.15: 6 Dihedral angle restraints: 10170 sinusoidal: 4146 harmonic: 6024 Sorted by residual: dihedral pdb=" CA ILE C 28 " pdb=" C ILE C 28 " pdb=" N ASN C 29 " pdb=" CA ASN C 29 " ideal model delta harmonic sigma weight residual 180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ILE F 28 " pdb=" C ILE F 28 " pdb=" N ASN F 29 " pdb=" CA ASN F 29 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ILE E 28 " pdb=" C ILE E 28 " pdb=" N ASN E 29 " pdb=" CA ASN E 29 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 10167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1253 0.029 - 0.057: 852 0.057 - 0.086: 301 0.086 - 0.115: 165 0.115 - 0.143: 63 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CA ILE D 323 " pdb=" N ILE D 323 " pdb=" C ILE D 323 " pdb=" CB ILE D 323 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE F 323 " pdb=" N ILE F 323 " pdb=" C ILE F 323 " pdb=" CB ILE F 323 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE A 323 " pdb=" N ILE A 323 " pdb=" C ILE A 323 " pdb=" CB ILE A 323 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2631 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 296 " 0.004 2.00e-02 2.50e+03 8.46e-03 7.15e-01 pdb=" C ILE F 296 " -0.015 2.00e-02 2.50e+03 pdb=" O ILE F 296 " 0.006 2.00e-02 2.50e+03 pdb=" N ASP F 297 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " -0.004 2.00e-02 2.50e+03 8.31e-03 6.91e-01 pdb=" C ILE A 296 " 0.014 2.00e-02 2.50e+03 pdb=" O ILE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP A 297 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 296 " -0.004 2.00e-02 2.50e+03 8.30e-03 6.88e-01 pdb=" C ILE B 296 " 0.014 2.00e-02 2.50e+03 pdb=" O ILE B 296 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP B 297 " -0.005 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 4861 2.82 - 3.34: 14609 3.34 - 3.86: 29436 3.86 - 4.38: 35184 4.38 - 4.90: 58991 Nonbonded interactions: 143081 Sorted by model distance: nonbonded pdb=" O LYS F 335 " pdb=" ND1 HIS F 338 " model vdw 2.294 3.120 nonbonded pdb=" O LYS A 335 " pdb=" ND1 HIS A 338 " model vdw 2.294 3.120 nonbonded pdb=" O LYS C 335 " pdb=" ND1 HIS C 338 " model vdw 2.294 3.120 nonbonded pdb=" O LYS B 335 " pdb=" ND1 HIS B 338 " model vdw 2.294 3.120 nonbonded pdb=" O LYS E 335 " pdb=" ND1 HIS E 338 " model vdw 2.295 3.120 ... (remaining 143076 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.730 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16872 Z= 0.242 Angle : 0.578 5.594 22902 Z= 0.305 Chirality : 0.048 0.143 2634 Planarity : 0.003 0.020 2922 Dihedral : 13.961 147.153 6282 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.93 % Allowed : 4.56 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2064 helix: 0.66 (0.23), residues: 522 sheet: 1.00 (0.30), residues: 318 loop : 0.10 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 258 TYR 0.012 0.001 TYR F 33 PHE 0.014 0.002 PHE F 269 TRP 0.004 0.001 TRP B 333 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.24 (16872) covalent geometry : angle 0.57757 / 0.30 (22902) hydrogen bonds : bond 0.14131 / 9.56 ( 612) hydrogen bonds : angle 6.74623 / 4.97 ( 1746) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.682 Fit side-chains REVERT: A 28 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 201 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7709 (tp) REVERT: A 217 LEU cc_start: 0.7255 (mp) cc_final: 0.7024 (mp) REVERT: A 233 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7529 (t80) REVERT: A 255 LEU cc_start: 0.8299 (mp) cc_final: 0.7924 (mm) REVERT: A 343 TYR cc_start: 0.7035 (p90) cc_final: 0.5752 (p90) REVERT: B 28 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 200 ASN cc_start: 0.8048 (t0) cc_final: 0.7843 (t0) REVERT: B 201 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7689 (tp) REVERT: B 217 LEU cc_start: 0.7253 (mp) cc_final: 0.6993 (mp) REVERT: B 233 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 255 LEU cc_start: 0.8260 (mp) cc_final: 0.7891 (mm) REVERT: B 343 TYR cc_start: 0.7055 (p90) cc_final: 0.6235 (p90) REVERT: C 28 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8089 (mm) REVERT: C 201 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 223 ILE cc_start: 0.7223 (mt) cc_final: 0.6909 (OUTLIER) REVERT: C 233 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7525 (t80) REVERT: C 255 LEU cc_start: 0.8277 (mp) cc_final: 0.7906 (mm) REVERT: C 343 TYR cc_start: 0.6997 (p90) cc_final: 0.6035 (p90) REVERT: D 28 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7936 (mm) REVERT: D 307 ILE cc_start: 0.8481 (tt) cc_final: 0.8090 (pt) REVERT: D 333 TRP cc_start: 0.7434 (m100) cc_final: 0.7056 (m100) REVERT: D 343 TYR cc_start: 0.8427 (p90) cc_final: 0.8114 (p90) REVERT: E 28 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7911 (mm) REVERT: E 233 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8031 (t80) REVERT: E 307 ILE cc_start: 0.8512 (tt) cc_final: 0.8118 (pt) REVERT: E 333 TRP cc_start: 0.7364 (m100) cc_final: 0.6949 (m100) REVERT: F 28 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7909 (mm) REVERT: F 307 ILE cc_start: 0.8536 (tt) cc_final: 0.8104 (pt) outliers start: 54 outliers final: 24 residues processed: 323 average time/residue: 0.5981 time to fit residues: 214.6014 Evaluate side-chains 215 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 235 HIS A 310 GLN B 310 GLN C 310 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101652 restraints weight = 21653.810| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.76 r_work: 0.3223 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16872 Z= 0.113 Angle : 0.518 5.097 22902 Z= 0.273 Chirality : 0.048 0.295 2634 Planarity : 0.003 0.020 2922 Dihedral : 10.744 143.814 2421 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.64 % Allowed : 10.97 % Favored : 85.40 % 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: 0.77 (0.19), residues: 2064 helix: 0.86 (0.23), residues: 534 sheet: 1.33 (0.31), residues: 324 loop : 0.22 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 258 TYR 0.008 0.001 TYR E 226 PHE 0.009 0.001 PHE D 269 TRP 0.003 0.001 TRP D 333 HIS 0.011 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (16872) covalent geometry : angle 0.51796 / 0.27 (22902) hydrogen bonds : bond 0.03504 / 2.31 ( 612) hydrogen bonds : angle 5.41551 / 3.93 ( 1746) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8412 (mtpt) REVERT: A 219 MET cc_start: 0.6962 (ttm) cc_final: 0.6670 (ttp) REVERT: A 233 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7119 (t80) REVERT: A 234 GLU cc_start: 0.7243 (mp0) cc_final: 0.7033 (mp0) REVERT: A 255 LEU cc_start: 0.8137 (mp) cc_final: 0.7869 (tp) REVERT: A 259 PHE cc_start: 0.7732 (t80) cc_final: 0.7497 (t80) REVERT: A 331 MET cc_start: 0.7301 (ttm) cc_final: 0.7035 (ttt) REVERT: A 333 TRP cc_start: 0.6798 (m100) cc_final: 0.6284 (m-90) REVERT: A 343 TYR cc_start: 0.7124 (p90) cc_final: 0.6538 (p90) REVERT: B 90 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8393 (mtpt) REVERT: B 200 ASN cc_start: 0.8293 (t0) cc_final: 0.7945 (t0) REVERT: B 233 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 255 LEU cc_start: 0.8140 (mp) cc_final: 0.7859 (tp) REVERT: B 322 THR cc_start: 0.7841 (t) cc_final: 0.7626 (m) REVERT: B 331 MET cc_start: 0.7365 (ttm) cc_final: 0.7104 (ttt) REVERT: B 343 TYR cc_start: 0.7089 (p90) cc_final: 0.6496 (p90) REVERT: C 90 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8454 (mttp) REVERT: C 219 MET cc_start: 0.6888 (ttm) cc_final: 0.6520 (ttp) REVERT: C 233 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7267 (t80) REVERT: C 234 GLU cc_start: 0.7262 (mp0) cc_final: 0.7028 (mp0) REVERT: C 255 LEU cc_start: 0.8121 (mp) cc_final: 0.7856 (tp) REVERT: C 322 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7585 (m) REVERT: C 331 MET cc_start: 0.7253 (ttm) cc_final: 0.7044 (ttt) REVERT: C 333 TRP cc_start: 0.6801 (m100) cc_final: 0.6280 (m-90) REVERT: C 343 TYR cc_start: 0.7058 (p90) cc_final: 0.6429 (p90) REVERT: D 205 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8532 (mtmm) REVERT: D 265 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: D 307 ILE cc_start: 0.8280 (tt) cc_final: 0.7697 (pt) REVERT: D 333 TRP cc_start: 0.7543 (m100) cc_final: 0.7052 (m100) REVERT: E 150 LYS cc_start: 0.8143 (pmtt) cc_final: 0.7894 (mtmm) REVERT: E 205 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: E 233 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8200 (t80) REVERT: E 265 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: E 307 ILE cc_start: 0.8325 (tt) cc_final: 0.7757 (pt) REVERT: E 333 TRP cc_start: 0.7446 (m100) cc_final: 0.6923 (m100) REVERT: F 133 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8457 (t70) REVERT: F 189 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7634 (mm110) REVERT: F 205 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8461 (mtmm) REVERT: F 265 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: F 307 ILE cc_start: 0.8339 (tt) cc_final: 0.7713 (pt) outliers start: 67 outliers final: 28 residues processed: 261 average time/residue: 0.5639 time to fit residues: 164.4292 Evaluate side-chains 219 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [58, 61, 157, 33, 178, 145, 169, 48, 72, 181, 184] chunk 58 optimal weight: 40.0000 chunk 61 optimal weight: 0.0770 chunk 157 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102121 restraints weight = 23202.984| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.69 r_work: 0.3254 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16872 Z= 0.159 Angle : 0.521 4.787 22902 Z= 0.276 Chirality : 0.048 0.293 2634 Planarity : 0.003 0.027 2922 Dihedral : 10.405 146.488 2395 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.18 % Allowed : 11.94 % Favored : 83.88 % 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: 0.62 (0.18), residues: 2064 helix: 0.77 (0.22), residues: 534 sheet: 1.34 (0.31), residues: 324 loop : 0.07 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.010 0.001 TYR F 33 PHE 0.012 0.001 PHE D 269 TRP 0.004 0.001 TRP E 333 HIS 0.006 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (16872) covalent geometry : angle 0.52082 / 0.28 (22902) hydrogen bonds : bond 0.03784 / 2.50 ( 612) hydrogen bonds : angle 5.30864 / 3.85 ( 1746) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 179 time to evaluate : 0.693 Fit side-chains REVERT: A 219 MET cc_start: 0.7007 (ttm) cc_final: 0.6692 (ttp) REVERT: A 233 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7144 (t80) REVERT: A 255 LEU cc_start: 0.8267 (mp) cc_final: 0.8007 (tp) REVERT: A 331 MET cc_start: 0.7241 (ttm) cc_final: 0.6995 (ttt) REVERT: A 333 TRP cc_start: 0.6862 (m100) cc_final: 0.5592 (m-10) REVERT: A 343 TYR cc_start: 0.7095 (p90) cc_final: 0.6724 (p90) REVERT: B 200 ASN cc_start: 0.8461 (t0) cc_final: 0.8084 (t0) REVERT: B 201 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7419 (tm) REVERT: B 202 GLN cc_start: 0.7785 (mp10) cc_final: 0.7563 (mp10) REVERT: B 212 ILE cc_start: 0.7967 (mt) cc_final: 0.7746 (mp) REVERT: B 219 MET cc_start: 0.6903 (ttm) cc_final: 0.6591 (ttt) REVERT: B 233 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6934 (t80) REVERT: B 255 LEU cc_start: 0.8264 (mp) cc_final: 0.7960 (tp) REVERT: B 331 MET cc_start: 0.7353 (ttm) cc_final: 0.7037 (ttt) REVERT: B 343 TYR cc_start: 0.7058 (p90) cc_final: 0.6626 (p90) REVERT: C 90 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8431 (mtpt) REVERT: C 233 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7178 (t80) REVERT: C 255 LEU cc_start: 0.8275 (mp) cc_final: 0.7988 (tp) REVERT: C 322 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7679 (m) REVERT: C 331 MET cc_start: 0.7151 (ttm) cc_final: 0.6881 (ttt) REVERT: C 333 TRP cc_start: 0.6885 (m100) cc_final: 0.6197 (m-90) REVERT: C 343 TYR cc_start: 0.7155 (p90) cc_final: 0.6649 (p90) REVERT: D 189 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7622 (mm-40) REVERT: D 205 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8557 (mtmm) REVERT: D 307 ILE cc_start: 0.8381 (tt) cc_final: 0.7800 (pt) REVERT: D 333 TRP cc_start: 0.7603 (m100) cc_final: 0.7123 (m100) REVERT: E 189 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7602 (mm-40) REVERT: E 205 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8582 (mtmm) REVERT: E 233 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8142 (t80) REVERT: E 307 ILE cc_start: 0.8375 (tt) cc_final: 0.7817 (pt) REVERT: E 333 TRP cc_start: 0.7519 (m100) cc_final: 0.6974 (m100) REVERT: F 189 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7586 (mm110) REVERT: F 205 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: F 307 ILE cc_start: 0.8370 (tt) cc_final: 0.7777 (pt) outliers start: 77 outliers final: 36 residues processed: 232 average time/residue: 0.5410 time to fit residues: 141.1111 Evaluate side-chains 219 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [190, 45, 60, 201, 187, 29, 159, 147, 61, 150, 54] chunk 190 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 159 optimal weight: 0.4980 chunk 147 optimal weight: 0.2980 chunk 61 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.140027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099793 restraints weight = 21843.388| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.77 r_work: 0.3191 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16872 Z= 0.153 Angle : 0.516 4.842 22902 Z= 0.273 Chirality : 0.048 0.292 2634 Planarity : 0.003 0.031 2922 Dihedral : 10.283 146.206 2391 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.07 % Allowed : 12.76 % Favored : 83.17 % 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: 0.56 (0.18), residues: 2064 helix: 0.69 (0.22), residues: 540 sheet: 1.38 (0.31), residues: 324 loop : 0.01 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.009 0.001 TYR C 194 PHE 0.012 0.001 PHE D 269 TRP 0.009 0.001 TRP B 333 HIS 0.007 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16872) covalent geometry : angle 0.51587 / 0.27 (22902) hydrogen bonds : bond 0.03600 / 2.38 ( 612) hydrogen bonds : angle 5.17805 / 3.75 ( 1746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 0.715 Fit side-chains REVERT: A 219 MET cc_start: 0.6903 (ttm) cc_final: 0.6680 (ttp) REVERT: A 223 ILE cc_start: 0.7045 (mt) cc_final: 0.6812 (pt) REVERT: A 233 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6856 (t80) REVERT: A 255 LEU cc_start: 0.8191 (mp) cc_final: 0.7917 (tp) REVERT: A 265 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: A 331 MET cc_start: 0.7237 (ttm) cc_final: 0.7021 (ttt) REVERT: A 343 TYR cc_start: 0.7076 (p90) cc_final: 0.6639 (p90) REVERT: B 200 ASN cc_start: 0.8463 (t0) cc_final: 0.8053 (t0) REVERT: B 201 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7441 (tm) REVERT: B 202 GLN cc_start: 0.7802 (mp10) cc_final: 0.7577 (mp10) REVERT: B 219 MET cc_start: 0.6924 (ttm) cc_final: 0.6723 (ttp) REVERT: B 255 LEU cc_start: 0.8233 (mp) cc_final: 0.7924 (tp) REVERT: B 265 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: B 331 MET cc_start: 0.7341 (ttm) cc_final: 0.7121 (ttt) REVERT: B 333 TRP cc_start: 0.6803 (m100) cc_final: 0.6297 (m-90) REVERT: B 343 TYR cc_start: 0.7067 (p90) cc_final: 0.6609 (p90) REVERT: C 90 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8416 (mttp) REVERT: C 212 ILE cc_start: 0.7934 (mt) cc_final: 0.7734 (mp) REVERT: C 223 ILE cc_start: 0.7028 (mt) cc_final: 0.6800 (pt) REVERT: C 233 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6961 (t80) REVERT: C 255 LEU cc_start: 0.8228 (mp) cc_final: 0.7923 (tp) REVERT: C 331 MET cc_start: 0.7239 (ttm) cc_final: 0.6935 (ttt) REVERT: C 343 TYR cc_start: 0.7074 (p90) cc_final: 0.6587 (p90) REVERT: D 189 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: D 205 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: D 265 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: D 307 ILE cc_start: 0.8344 (tt) cc_final: 0.7791 (pt) REVERT: D 333 TRP cc_start: 0.7581 (m100) cc_final: 0.7142 (m100) REVERT: E 189 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: E 205 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: E 233 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8089 (t80) REVERT: E 265 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: E 307 ILE cc_start: 0.8333 (tt) cc_final: 0.7763 (pt) REVERT: E 333 TRP cc_start: 0.7462 (m100) cc_final: 0.6936 (m100) REVERT: F 189 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7727 (mm110) REVERT: F 205 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: F 307 ILE cc_start: 0.8351 (tt) cc_final: 0.7784 (pt) outliers start: 75 outliers final: 37 residues processed: 228 average time/residue: 0.5527 time to fit residues: 141.2879 Evaluate side-chains 213 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [141, 58, 119, 147, 72, 55, 169, 51, 149, 128, 172] chunk 141 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS B 338 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100880 restraints weight = 21699.398| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.77 r_work: 0.3214 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16872 Z= 0.113 Angle : 0.489 4.860 22902 Z= 0.259 Chirality : 0.047 0.291 2634 Planarity : 0.003 0.033 2922 Dihedral : 9.841 145.426 2385 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.23 % Allowed : 13.19 % Favored : 82.57 % 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: 0.64 (0.19), residues: 2064 helix: 0.84 (0.23), residues: 540 sheet: 1.47 (0.31), residues: 324 loop : 0.00 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.007 0.001 TYR F 33 PHE 0.010 0.001 PHE D 269 TRP 0.006 0.001 TRP A 333 HIS 0.013 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16872) covalent geometry : angle 0.48896 / 0.26 (22902) hydrogen bonds : bond 0.03174 / 2.11 ( 612) hydrogen bonds : angle 4.99279 / 3.61 ( 1746) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 176 time to evaluate : 0.647 Fit side-chains REVERT: A 28 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 219 MET cc_start: 0.6970 (ttm) cc_final: 0.6754 (ttp) REVERT: A 223 ILE cc_start: 0.7093 (mt) cc_final: 0.6874 (pt) REVERT: A 238 TYR cc_start: 0.6444 (m-80) cc_final: 0.6240 (m-80) REVERT: A 255 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7954 (tp) REVERT: A 265 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: A 331 MET cc_start: 0.7217 (ttm) cc_final: 0.7002 (ttt) REVERT: A 333 TRP cc_start: 0.6948 (m100) cc_final: 0.5655 (m-10) REVERT: A 343 TYR cc_start: 0.7111 (p90) cc_final: 0.6659 (p90) REVERT: B 28 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 200 ASN cc_start: 0.8446 (t0) cc_final: 0.8084 (t0) REVERT: B 201 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7716 (tm) REVERT: B 219 MET cc_start: 0.6971 (ttm) cc_final: 0.6749 (ttp) REVERT: B 255 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7948 (tp) REVERT: B 265 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: B 331 MET cc_start: 0.7270 (ttm) cc_final: 0.7058 (ttt) REVERT: B 333 TRP cc_start: 0.6915 (m100) cc_final: 0.6347 (m-90) REVERT: B 343 TYR cc_start: 0.7098 (p90) cc_final: 0.6628 (p90) REVERT: C 28 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (mm) REVERT: C 90 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8406 (mttp) REVERT: C 223 ILE cc_start: 0.7060 (mt) cc_final: 0.6728 (pp) REVERT: C 233 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7079 (t80) REVERT: C 255 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7943 (tp) REVERT: C 265 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: C 331 MET cc_start: 0.7221 (ttm) cc_final: 0.6984 (ttt) REVERT: C 333 TRP cc_start: 0.6949 (m100) cc_final: 0.6286 (m-90) REVERT: C 343 TYR cc_start: 0.7098 (p90) cc_final: 0.6595 (p90) REVERT: D 205 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8532 (mtmm) REVERT: D 265 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: D 307 ILE cc_start: 0.8400 (tt) cc_final: 0.7840 (pt) REVERT: D 333 TRP cc_start: 0.7679 (m100) cc_final: 0.7250 (m100) REVERT: E 205 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8569 (mtmm) REVERT: E 265 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: E 307 ILE cc_start: 0.8359 (tt) cc_final: 0.7812 (pt) REVERT: E 333 TRP cc_start: 0.7552 (m100) cc_final: 0.7032 (m100) REVERT: F 189 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7722 (mm110) REVERT: F 205 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8442 (mtmm) REVERT: F 307 ILE cc_start: 0.8394 (tt) cc_final: 0.7830 (pt) outliers start: 78 outliers final: 27 residues processed: 232 average time/residue: 0.5268 time to fit residues: 137.3809 Evaluate side-chains 208 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [172, 84, 34, 110, 170, 193, 138, 41, 144, 13, 163] chunk 172 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 HIS B 338 HIS D 29 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100327 restraints weight = 21960.566| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.87 r_work: 0.3171 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16872 Z= 0.211 Angle : 0.571 7.056 22902 Z= 0.300 Chirality : 0.050 0.300 2634 Planarity : 0.003 0.033 2922 Dihedral : 10.018 147.833 2375 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.67 % Allowed : 13.52 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.37 (0.18), residues: 2064 helix: 0.49 (0.22), residues: 540 sheet: 1.33 (0.31), residues: 324 loop : -0.11 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 258 TYR 0.010 0.002 TYR F 33 PHE 0.015 0.002 PHE D 269 TRP 0.005 0.001 TRP B 333 HIS 0.009 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (16872) covalent geometry : angle 0.57089 / 0.30 (22902) hydrogen bonds : bond 0.03966 / 2.63 ( 612) hydrogen bonds : angle 5.31288 / 3.86 ( 1746) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 165 time to evaluate : 0.669 Fit side-chains REVERT: A 28 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8323 (mm) REVERT: A 105 MET cc_start: 0.8825 (mmm) cc_final: 0.8617 (mmt) REVERT: A 219 MET cc_start: 0.6919 (ttm) cc_final: 0.6594 (ttp) REVERT: A 255 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 265 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: A 331 MET cc_start: 0.7231 (ttm) cc_final: 0.6951 (ttt) REVERT: A 343 TYR cc_start: 0.7079 (p90) cc_final: 0.6694 (p90) REVERT: B 28 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 200 ASN cc_start: 0.8480 (t0) cc_final: 0.8080 (t0) REVERT: B 201 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7608 (tm) REVERT: B 202 GLN cc_start: 0.7803 (mp10) cc_final: 0.7597 (mp10) REVERT: B 219 MET cc_start: 0.6904 (ttm) cc_final: 0.6672 (ttp) REVERT: B 235 HIS cc_start: 0.6407 (t-170) cc_final: 0.6102 (t70) REVERT: B 255 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7919 (tp) REVERT: B 265 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: B 343 TYR cc_start: 0.7070 (p90) cc_final: 0.6589 (p90) REVERT: C 233 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6807 (t80) REVERT: C 255 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 265 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: C 343 TYR cc_start: 0.7100 (p90) cc_final: 0.6642 (p90) REVERT: D 45 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: D 205 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8531 (mtmm) REVERT: D 307 ILE cc_start: 0.8402 (tt) cc_final: 0.7818 (pt) REVERT: D 333 TRP cc_start: 0.7510 (m100) cc_final: 0.7112 (m100) REVERT: D 341 THR cc_start: 0.7352 (OUTLIER) cc_final: 0.7033 (m) REVERT: E 205 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8539 (mtmm) REVERT: E 307 ILE cc_start: 0.8346 (tt) cc_final: 0.7796 (pt) REVERT: E 333 TRP cc_start: 0.7394 (m100) cc_final: 0.6887 (m100) REVERT: F 189 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7704 (mm110) REVERT: F 205 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8441 (mtmm) REVERT: F 307 ILE cc_start: 0.8370 (tt) cc_final: 0.7814 (pt) outliers start: 86 outliers final: 36 residues processed: 227 average time/residue: 0.5411 time to fit residues: 137.6976 Evaluate side-chains 208 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [19, 50, 120, 21, 93, 7, 28, 102, 181, 114, 57] chunk 19 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS E 29 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100416 restraints weight = 21970.403| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3163 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16872 Z= 0.168 Angle : 0.552 7.067 22902 Z= 0.289 Chirality : 0.049 0.304 2634 Planarity : 0.003 0.036 2922 Dihedral : 9.970 147.403 2375 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.80 % Allowed : 15.04 % Favored : 81.16 % 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: 0.33 (0.18), residues: 2064 helix: 0.50 (0.22), residues: 540 sheet: 1.27 (0.30), residues: 324 loop : -0.14 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.008 0.001 TYR A 231 PHE 0.013 0.001 PHE D 269 TRP 0.012 0.001 TRP B 333 HIS 0.010 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (16872) covalent geometry : angle 0.55245 / 0.29 (22902) hydrogen bonds : bond 0.03685 / 2.44 ( 612) hydrogen bonds : angle 5.23615 / 3.81 ( 1746) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 160 time to evaluate : 0.636 Fit side-chains REVERT: A 28 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 105 MET cc_start: 0.8845 (mmm) cc_final: 0.8624 (mmt) REVERT: A 219 MET cc_start: 0.6936 (ttm) cc_final: 0.6585 (ttp) REVERT: A 255 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 265 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: A 331 MET cc_start: 0.7234 (ttm) cc_final: 0.6993 (ttt) REVERT: A 333 TRP cc_start: 0.6870 (m100) cc_final: 0.6344 (m-90) REVERT: A 343 TYR cc_start: 0.7101 (p90) cc_final: 0.6705 (p90) REVERT: B 28 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8279 (mm) REVERT: B 200 ASN cc_start: 0.8491 (t0) cc_final: 0.8100 (t0) REVERT: B 201 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7637 (tm) REVERT: B 202 GLN cc_start: 0.7820 (mp10) cc_final: 0.7590 (mp10) REVERT: B 235 HIS cc_start: 0.6459 (t-170) cc_final: 0.6154 (t-90) REVERT: B 255 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 265 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7076 (mm-30) REVERT: B 331 MET cc_start: 0.7043 (ttm) cc_final: 0.6823 (ttt) REVERT: B 333 TRP cc_start: 0.6860 (m100) cc_final: 0.6485 (m-90) REVERT: B 343 TYR cc_start: 0.7019 (p90) cc_final: 0.6696 (p90) REVERT: C 28 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8212 (mm) REVERT: C 233 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6812 (t80) REVERT: C 255 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7941 (tp) REVERT: C 265 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: C 333 TRP cc_start: 0.6968 (m100) cc_final: 0.6302 (m-90) REVERT: C 343 TYR cc_start: 0.6962 (p90) cc_final: 0.6585 (p90) REVERT: D 205 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (mtmm) REVERT: D 307 ILE cc_start: 0.8403 (tt) cc_final: 0.7837 (pt) REVERT: D 333 TRP cc_start: 0.7543 (m100) cc_final: 0.7086 (m100) REVERT: D 341 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7035 (m) REVERT: E 205 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: E 233 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8021 (t80) REVERT: E 307 ILE cc_start: 0.8347 (tt) cc_final: 0.7803 (pt) REVERT: E 331 MET cc_start: 0.7626 (tpp) cc_final: 0.7239 (tpp) REVERT: E 333 TRP cc_start: 0.7420 (m100) cc_final: 0.6845 (m100) REVERT: E 341 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.6992 (m) REVERT: F 189 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7739 (mm110) REVERT: F 205 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8455 (mtmm) REVERT: F 307 ILE cc_start: 0.8380 (tt) cc_final: 0.7830 (pt) outliers start: 70 outliers final: 39 residues processed: 211 average time/residue: 0.5453 time to fit residues: 129.2845 Evaluate side-chains 213 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 156 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [161, 138, 70, 73, 74, 130, 20, 96, 39, 9, 143] chunk 161 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 overall best weight: 7.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.139597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103407 restraints weight = 22715.118| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.67 r_work: 0.3217 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16872 Z= 0.203 Angle : 0.580 8.479 22902 Z= 0.303 Chirality : 0.050 0.312 2634 Planarity : 0.004 0.038 2922 Dihedral : 10.198 149.439 2375 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.85 % Allowed : 15.58 % Favored : 80.56 % 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: 0.25 (0.18), residues: 2064 helix: 0.40 (0.22), residues: 540 sheet: 1.18 (0.30), residues: 324 loop : -0.17 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.009 0.002 TYR A 231 PHE 0.014 0.002 PHE D 269 TRP 0.010 0.001 TRP B 333 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (16872) covalent geometry : angle 0.57985 / 0.30 (22902) hydrogen bonds : bond 0.03937 / 2.61 ( 612) hydrogen bonds : angle 5.34130 / 3.88 ( 1746) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 159 time to evaluate : 0.647 Fit side-chains REVERT: A 28 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 105 MET cc_start: 0.8831 (mmm) cc_final: 0.8620 (mmt) REVERT: A 219 MET cc_start: 0.7029 (ttm) cc_final: 0.6676 (ttp) REVERT: A 255 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 265 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: A 331 MET cc_start: 0.7200 (ttm) cc_final: 0.6903 (ttt) REVERT: A 343 TYR cc_start: 0.7108 (p90) cc_final: 0.6717 (p90) REVERT: B 28 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8315 (mm) REVERT: B 200 ASN cc_start: 0.8484 (t0) cc_final: 0.8102 (t0) REVERT: B 201 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7718 (tm) REVERT: B 202 GLN cc_start: 0.7786 (mp10) cc_final: 0.7571 (mp10) REVERT: B 235 HIS cc_start: 0.6505 (t-170) cc_final: 0.6198 (t-90) REVERT: B 255 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7987 (tp) REVERT: B 265 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: B 331 MET cc_start: 0.7092 (ttm) cc_final: 0.6866 (ttt) REVERT: B 333 TRP cc_start: 0.6909 (m100) cc_final: 0.6456 (m-90) REVERT: B 343 TYR cc_start: 0.7066 (p90) cc_final: 0.6778 (p90) REVERT: C 233 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6769 (t80) REVERT: C 255 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7986 (tp) REVERT: C 265 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: C 331 MET cc_start: 0.7043 (ttt) cc_final: 0.6720 (ttt) REVERT: C 333 TRP cc_start: 0.6973 (m100) cc_final: 0.6513 (m-90) REVERT: C 343 TYR cc_start: 0.7051 (p90) cc_final: 0.6623 (p90) REVERT: D 205 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8540 (mtmm) REVERT: D 307 ILE cc_start: 0.8451 (tt) cc_final: 0.7888 (pt) REVERT: D 331 MET cc_start: 0.7519 (tpp) cc_final: 0.7187 (tpp) REVERT: D 333 TRP cc_start: 0.7528 (m100) cc_final: 0.7015 (m100) REVERT: E 45 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: E 205 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: E 233 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8033 (t80) REVERT: E 307 ILE cc_start: 0.8391 (tt) cc_final: 0.7864 (pt) REVERT: E 333 TRP cc_start: 0.7467 (m100) cc_final: 0.7029 (m100) REVERT: F 189 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7652 (mm110) REVERT: F 205 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8437 (mtmm) REVERT: F 307 ILE cc_start: 0.8428 (tt) cc_final: 0.7893 (pt) outliers start: 71 outliers final: 40 residues processed: 209 average time/residue: 0.5522 time to fit residues: 129.2951 Evaluate side-chains 213 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [16, 4, 198, 31, 89, 185, 24, 130, 168, 86, 90] chunk 16 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106047 restraints weight = 22649.376| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.65 r_work: 0.3257 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16872 Z= 0.136 Angle : 0.536 7.792 22902 Z= 0.281 Chirality : 0.048 0.311 2634 Planarity : 0.003 0.040 2922 Dihedral : 9.937 149.748 2375 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.58 % Allowed : 16.34 % Favored : 80.08 % 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: 2064 helix: 0.59 (0.23), residues: 540 sheet: 1.25 (0.30), residues: 324 loop : -0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.008 0.001 TYR F 226 PHE 0.010 0.001 PHE D 269 TRP 0.013 0.001 TRP A 333 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16872) covalent geometry : angle 0.53584 / 0.28 (22902) hydrogen bonds : bond 0.03399 / 2.27 ( 612) hydrogen bonds : angle 5.12476 / 3.72 ( 1746) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 0.536 Fit side-chains REVERT: A 28 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8145 (mm) REVERT: A 105 MET cc_start: 0.8827 (mmm) cc_final: 0.8625 (mmt) REVERT: A 219 MET cc_start: 0.7028 (ttm) cc_final: 0.6705 (ttp) REVERT: A 223 ILE cc_start: 0.7078 (mt) cc_final: 0.6824 (pt) REVERT: A 238 TYR cc_start: 0.6467 (m-80) cc_final: 0.6182 (m-80) REVERT: A 255 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7929 (tp) REVERT: A 265 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: A 331 MET cc_start: 0.7198 (ttm) cc_final: 0.6956 (ttt) REVERT: A 333 TRP cc_start: 0.6910 (m100) cc_final: 0.6453 (m-90) REVERT: A 343 TYR cc_start: 0.7074 (p90) cc_final: 0.6676 (p90) REVERT: B 28 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 200 ASN cc_start: 0.8458 (t0) cc_final: 0.8074 (t0) REVERT: B 201 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7687 (tm) REVERT: B 202 GLN cc_start: 0.7763 (mp10) cc_final: 0.7542 (mp10) REVERT: B 235 HIS cc_start: 0.6556 (t-170) cc_final: 0.6254 (t70) REVERT: B 255 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7957 (tp) REVERT: B 265 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: B 331 MET cc_start: 0.7066 (ttm) cc_final: 0.6839 (ttt) REVERT: B 333 TRP cc_start: 0.6923 (m100) cc_final: 0.6494 (m-90) REVERT: B 343 TYR cc_start: 0.7050 (p90) cc_final: 0.6768 (p90) REVERT: C 28 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8090 (mm) REVERT: C 255 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7984 (tp) REVERT: C 265 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: C 331 MET cc_start: 0.7035 (ttt) cc_final: 0.6712 (ttt) REVERT: C 333 TRP cc_start: 0.6963 (m100) cc_final: 0.6437 (m-90) REVERT: C 343 TYR cc_start: 0.7078 (p90) cc_final: 0.6661 (p90) REVERT: D 205 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: D 307 ILE cc_start: 0.8455 (tt) cc_final: 0.7908 (pt) REVERT: D 331 MET cc_start: 0.7494 (tpp) cc_final: 0.7117 (tpp) REVERT: D 333 TRP cc_start: 0.7585 (m100) cc_final: 0.7021 (m100) REVERT: E 205 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8530 (mtmm) REVERT: E 233 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8022 (t80) REVERT: E 265 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: E 307 ILE cc_start: 0.8389 (tt) cc_final: 0.7863 (pt) REVERT: E 331 MET cc_start: 0.7542 (tpp) cc_final: 0.7224 (tpp) REVERT: E 333 TRP cc_start: 0.7470 (m100) cc_final: 0.6893 (m100) REVERT: F 189 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7632 (mm110) REVERT: F 205 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8449 (mtmm) REVERT: F 307 ILE cc_start: 0.8424 (tt) cc_final: 0.7886 (pt) outliers start: 66 outliers final: 36 residues processed: 211 average time/residue: 0.5522 time to fit residues: 130.6167 Evaluate side-chains 212 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [60, 56, 36, 5, 70, 171, 102, 77, 192, 55, 0] chunk 60 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 77 optimal weight: 0.0970 chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.103601 restraints weight = 22656.550| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.68 r_work: 0.3259 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16872 Z= 0.133 Angle : 0.536 7.450 22902 Z= 0.281 Chirality : 0.048 0.311 2634 Planarity : 0.003 0.038 2922 Dihedral : 9.748 149.991 2373 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.04 % Allowed : 16.72 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2064 helix: 0.61 (0.23), residues: 540 sheet: 1.19 (0.33), residues: 294 loop : -0.11 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 207 TYR 0.007 0.001 TYR F 226 PHE 0.011 0.001 PHE D 269 TRP 0.011 0.001 TRP A 333 HIS 0.007 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (16872) covalent geometry : angle 0.53635 / 0.28 (22902) hydrogen bonds : bond 0.03360 / 2.24 ( 612) hydrogen bonds : angle 5.11546 / 3.72 ( 1746) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.660 Fit side-chains REVERT: A 28 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8151 (mm) REVERT: A 219 MET cc_start: 0.6968 (ttm) cc_final: 0.6614 (ttp) REVERT: A 223 ILE cc_start: 0.7055 (mt) cc_final: 0.6812 (pt) REVERT: A 238 TYR cc_start: 0.6429 (m-80) cc_final: 0.6135 (m-80) REVERT: A 255 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 265 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: A 331 MET cc_start: 0.7174 (ttm) cc_final: 0.6893 (ttt) REVERT: A 333 TRP cc_start: 0.6889 (m100) cc_final: 0.6472 (m-90) REVERT: A 343 TYR cc_start: 0.7050 (p90) cc_final: 0.6635 (p90) REVERT: B 28 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 200 ASN cc_start: 0.8452 (t0) cc_final: 0.8087 (t0) REVERT: B 201 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7852 (tm) REVERT: B 235 HIS cc_start: 0.6469 (t-170) cc_final: 0.6192 (t-90) REVERT: B 255 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7907 (tp) REVERT: B 331 MET cc_start: 0.7080 (ttm) cc_final: 0.6852 (ttt) REVERT: B 333 TRP cc_start: 0.6895 (m100) cc_final: 0.6474 (m-90) REVERT: B 343 TYR cc_start: 0.7015 (p90) cc_final: 0.6616 (p90) REVERT: C 28 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8105 (mm) REVERT: C 200 ASN cc_start: 0.7981 (t0) cc_final: 0.7778 (t0) REVERT: C 255 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (tp) REVERT: C 265 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 331 MET cc_start: 0.7093 (ttt) cc_final: 0.6790 (ttt) REVERT: C 333 TRP cc_start: 0.6951 (m100) cc_final: 0.6329 (m-90) REVERT: C 343 TYR cc_start: 0.7062 (p90) cc_final: 0.6651 (p90) REVERT: D 45 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8456 (tp30) REVERT: D 205 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: D 265 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: D 307 ILE cc_start: 0.8428 (tt) cc_final: 0.7886 (pt) REVERT: D 331 MET cc_start: 0.7449 (tpp) cc_final: 0.7060 (tpp) REVERT: D 333 TRP cc_start: 0.7537 (m100) cc_final: 0.7029 (m100) REVERT: E 205 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8554 (mtmm) REVERT: E 233 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8031 (t80) REVERT: E 265 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: E 307 ILE cc_start: 0.8364 (tt) cc_final: 0.7834 (pt) REVERT: E 331 MET cc_start: 0.7528 (tpp) cc_final: 0.7187 (tpp) REVERT: E 333 TRP cc_start: 0.7453 (m100) cc_final: 0.6953 (m100) REVERT: F 189 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7632 (mm110) REVERT: F 205 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8449 (mtmm) REVERT: F 307 ILE cc_start: 0.8406 (tt) cc_final: 0.7861 (pt) REVERT: F 331 MET cc_start: 0.7561 (tpp) cc_final: 0.7223 (tpp) outliers start: 56 outliers final: 28 residues processed: 200 average time/residue: 0.5474 time to fit residues: 122.9298 Evaluate side-chains 205 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 205 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: [108, 13, 140, 156, 144, 182, 87, 134, 171, 124, 148] chunk 108 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 140 optimal weight: 0.0270 chunk 156 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105200 restraints weight = 22497.692| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.58 r_work: 0.3251 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16872 Z= 0.157 Angle : 0.552 7.309 22902 Z= 0.289 Chirality : 0.049 0.310 2634 Planarity : 0.003 0.037 2922 Dihedral : 9.801 150.705 2370 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.99 % Allowed : 16.61 % Favored : 80.40 % 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: 0.36 (0.18), residues: 2064 helix: 0.51 (0.23), residues: 540 sheet: 1.27 (0.30), residues: 324 loop : -0.12 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 258 TYR 0.008 0.001 TYR A 231 PHE 0.012 0.001 PHE D 269 TRP 0.012 0.001 TRP F 333 HIS 0.007 0.001 HIS D 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16872) covalent geometry : angle 0.55224 / 0.29 (22902) hydrogen bonds : bond 0.03568 / 2.37 ( 612) hydrogen bonds : angle 5.21637 / 3.79 ( 1746) =============================================================================== Job complete usr+sys time: 7339.59 seconds wall clock time: 125 minutes 20.86 seconds (7520.86 seconds total)