Starting phenix.real_space_refine on Tue Dec 31 10:36:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266.map" model { file = "/net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gts_34266/12_2024/8gts_34266_neut.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 10290 2.51 5 N 2429 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15470 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2210 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.01, per 1000 atoms: 0.39 Number of scatterers: 15470 At special positions: 0 Unit cell: (105.93, 108.07, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2674 8.00 N 2429 7.00 C 10290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 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: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 69.8% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 296 Proline residue: A 289 - end of helix removed outlier: 3.622A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 296 Proline residue: B 289 - end of helix removed outlier: 3.622A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 99 through 131 removed outlier: 4.419A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 236 removed outlier: 3.648A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 221 " --> pdb=" O HIS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 296 Proline residue: C 289 - end of helix removed outlier: 3.622A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 removed outlier: 3.690A pdb=" N THR D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 9 " --> pdb=" O GLN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 221 " --> pdb=" O HIS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 296 Proline residue: D 289 - end of helix removed outlier: 3.623A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 removed outlier: 3.690A pdb=" N THR E 8 " --> pdb=" O ALA E 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU E 9 " --> pdb=" O GLN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU E 45 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.555A pdb=" N TYR E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU E 221 " --> pdb=" O HIS E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.976A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 296 Proline residue: E 289 - end of helix removed outlier: 3.623A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.738A pdb=" N TYR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.502A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU F 9 " --> pdb=" O GLN F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.419A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU F 221 " --> pdb=" O HIS F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 296 Proline residue: F 289 - end of helix removed outlier: 3.622A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU G 9 " --> pdb=" O GLN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU G 45 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 99 through 131 removed outlier: 4.421A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR G 199 " --> pdb=" O ILE G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 236 removed outlier: 3.650A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU G 221 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 296 Proline residue: G 289 - end of helix removed outlier: 3.623A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.771A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.769A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.769A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2751 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: 4.50 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4615 1.34 - 1.46: 3610 1.46 - 1.58: 7483 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 15799 Sorted by residual: bond pdb=" C LEU D 45 " pdb=" N PRO D 46 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.83e+00 bond pdb=" C LEU C 45 " pdb=" N PRO C 46 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C LEU A 45 " pdb=" N PRO A 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.75e+00 bond pdb=" C LEU E 45 " pdb=" N PRO E 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.74e+00 bond pdb=" C LEU F 45 " pdb=" N PRO F 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.73e+00 ... (remaining 15794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 20719 1.47 - 2.95: 585 2.95 - 4.42: 130 4.42 - 5.90: 77 5.90 - 7.37: 7 Bond angle restraints: 21518 Sorted by residual: angle pdb=" N ILE F 3 " pdb=" CA ILE F 3 " pdb=" C ILE F 3 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" N LYS B 140 " pdb=" CA LYS B 140 " pdb=" CB LYS B 140 " ideal model delta sigma weight residual 110.12 114.73 -4.61 1.47e+00 4.63e-01 9.82e+00 angle pdb=" N LYS D 140 " pdb=" CA LYS D 140 " pdb=" CB LYS D 140 " ideal model delta sigma weight residual 110.12 114.72 -4.60 1.47e+00 4.63e-01 9.78e+00 angle pdb=" N LYS A 140 " pdb=" CA LYS A 140 " pdb=" CB LYS A 140 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.67e+00 angle pdb=" N LYS G 140 " pdb=" CA LYS G 140 " pdb=" CB LYS G 140 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.66e+00 ... (remaining 21513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 8337 15.98 - 31.96: 724 31.96 - 47.94: 252 47.94 - 63.92: 49 63.92 - 79.90: 7 Dihedral angle restraints: 9369 sinusoidal: 3363 harmonic: 6006 Sorted by residual: dihedral pdb=" CA GLU C 352 " pdb=" C GLU C 352 " pdb=" N ASN C 353 " pdb=" CA ASN C 353 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU G 352 " pdb=" C GLU G 352 " pdb=" N ASN G 353 " pdb=" CA ASN G 353 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU A 352 " pdb=" C GLU A 352 " pdb=" N ASN A 353 " pdb=" CA ASN A 353 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 9366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1773 0.034 - 0.067: 637 0.067 - 0.101: 184 0.101 - 0.135: 52 0.135 - 0.168: 7 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CA GLU D 352 " pdb=" N GLU D 352 " pdb=" C GLU D 352 " pdb=" CB GLU D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA GLU B 352 " pdb=" N GLU B 352 " pdb=" C GLU B 352 " pdb=" CB GLU B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU A 352 " pdb=" N GLU A 352 " pdb=" C GLU A 352 " pdb=" CB GLU A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2650 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 123 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO B 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 123 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO E 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO C 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.019 5.00e-02 4.00e+02 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 106 2.60 - 3.18: 13798 3.18 - 3.75: 24018 3.75 - 4.33: 29508 4.33 - 4.90: 49014 Nonbonded interactions: 116444 Sorted by model distance: nonbonded pdb=" SG CYS B 84 " pdb=" SG CYS B 246 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS G 84 " pdb=" SG CYS G 246 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 84 " pdb=" SG CYS E 246 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 84 " pdb=" SG CYS F 246 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 84 " pdb=" SG CYS C 246 " model vdw 2.029 3.760 ... (remaining 116439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 32.540 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.003 0.036 15799 Z= 0.176 Angle : 0.672 7.374 21518 Z= 0.352 Chirality : 0.039 0.168 2653 Planarity : 0.004 0.033 2590 Dihedral : 14.162 79.903 5432 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.42 % Allowed : 0.12 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1946 helix: 1.30 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 104 HIS 0.001 0.001 HIS F 106 PHE 0.009 0.001 PHE F 116 TYR 0.019 0.001 TYR D 230 ARG 0.001 0.000 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 259 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7862 (m-30) cc_final: 0.7542 (m-30) REVERT: B 261 ASP cc_start: 0.7780 (m-30) cc_final: 0.7575 (p0) REVERT: C 37 MET cc_start: 0.6277 (tpp) cc_final: 0.5980 (tpp) REVERT: C 75 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7127 (tpp-160) REVERT: C 224 ILE cc_start: 0.7368 (mm) cc_final: 0.7157 (mt) REVERT: D 75 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7140 (tpp-160) REVERT: D 198 GLN cc_start: 0.7449 (mp-120) cc_final: 0.7197 (mp-120) REVERT: E 75 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6872 (tpp-160) REVERT: E 261 ASP cc_start: 0.7667 (m-30) cc_final: 0.7366 (m-30) REVERT: F 75 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7113 (tpp-160) REVERT: F 224 ILE cc_start: 0.7200 (mm) cc_final: 0.6989 (mt) REVERT: F 261 ASP cc_start: 0.7898 (m-30) cc_final: 0.7524 (m-30) REVERT: F 296 PHE cc_start: 0.7527 (m-10) cc_final: 0.7236 (m-10) REVERT: G 75 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7197 (tpp-160) REVERT: G 261 ASP cc_start: 0.7668 (m-30) cc_final: 0.7424 (p0) outliers start: 7 outliers final: 0 residues processed: 259 average time/residue: 0.2482 time to fit residues: 98.2478 Evaluate side-chains 222 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain G residue 75 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15799 Z= 0.203 Angle : 0.624 6.503 21518 Z= 0.311 Chirality : 0.040 0.127 2653 Planarity : 0.004 0.032 2590 Dihedral : 5.524 56.141 2120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.51 % Allowed : 12.05 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1946 helix: 1.31 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -2.12 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS G 217 PHE 0.012 0.001 PHE A 244 TYR 0.022 0.001 TYR D 121 ARG 0.001 0.000 ARG F 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.5462 (tpp) cc_final: 0.5127 (tpp) REVERT: A 261 ASP cc_start: 0.7790 (m-30) cc_final: 0.7506 (m-30) REVERT: A 334 PHE cc_start: 0.7179 (m-10) cc_final: 0.6819 (m-80) REVERT: B 334 PHE cc_start: 0.7127 (m-10) cc_final: 0.6708 (m-80) REVERT: C 37 MET cc_start: 0.6274 (tpp) cc_final: 0.5906 (tpp) REVERT: C 75 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7135 (tpp-160) REVERT: C 224 ILE cc_start: 0.7390 (mm) cc_final: 0.7115 (mt) REVERT: C 334 PHE cc_start: 0.7093 (m-10) cc_final: 0.6657 (m-80) REVERT: D 334 PHE cc_start: 0.6910 (m-10) cc_final: 0.6490 (m-80) REVERT: E 75 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6982 (tpp-160) REVERT: E 334 PHE cc_start: 0.7022 (m-10) cc_final: 0.6624 (m-80) REVERT: F 224 ILE cc_start: 0.7225 (mm) cc_final: 0.6993 (mt) REVERT: F 334 PHE cc_start: 0.7198 (m-10) cc_final: 0.6929 (m-80) REVERT: G 75 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7114 (tpp-160) REVERT: G 261 ASP cc_start: 0.7676 (m-30) cc_final: 0.7412 (p0) REVERT: G 334 PHE cc_start: 0.7061 (m-10) cc_final: 0.6833 (m-80) outliers start: 25 outliers final: 20 residues processed: 234 average time/residue: 0.2457 time to fit residues: 88.9121 Evaluate side-chains 227 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 347 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15799 Z= 0.211 Angle : 0.621 9.885 21518 Z= 0.303 Chirality : 0.040 0.124 2653 Planarity : 0.004 0.038 2590 Dihedral : 4.753 59.507 2112 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.21 % Allowed : 14.47 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1946 helix: 1.34 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.002 0.001 HIS A 134 PHE 0.010 0.001 PHE F 244 TYR 0.025 0.002 TYR F 121 ARG 0.001 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7189 (m-10) cc_final: 0.6850 (m-80) REVERT: B 334 PHE cc_start: 0.7092 (m-10) cc_final: 0.6665 (m-80) REVERT: C 37 MET cc_start: 0.6067 (tpp) cc_final: 0.5547 (tpp) REVERT: C 75 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6995 (tpp-160) REVERT: C 198 GLN cc_start: 0.7919 (mp-120) cc_final: 0.7472 (mp10) REVERT: C 334 PHE cc_start: 0.7125 (m-10) cc_final: 0.6673 (m-80) REVERT: D 334 PHE cc_start: 0.6952 (m-10) cc_final: 0.6536 (m-80) REVERT: E 334 PHE cc_start: 0.7213 (m-10) cc_final: 0.6844 (m-80) REVERT: F 198 GLN cc_start: 0.7607 (mp-120) cc_final: 0.6900 (mp10) REVERT: F 334 PHE cc_start: 0.7171 (m-10) cc_final: 0.6964 (m-80) REVERT: G 75 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7171 (tpp-160) REVERT: G 334 PHE cc_start: 0.7152 (m-10) cc_final: 0.6949 (m-80) outliers start: 53 outliers final: 35 residues processed: 262 average time/residue: 0.2463 time to fit residues: 99.6043 Evaluate side-chains 259 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15799 Z= 0.177 Angle : 0.622 11.484 21518 Z= 0.294 Chirality : 0.039 0.123 2653 Planarity : 0.004 0.038 2590 Dihedral : 4.282 59.308 2108 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.54 % Allowed : 17.68 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1946 helix: 1.59 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE A 244 TYR 0.024 0.002 TYR F 121 ARG 0.002 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7139 (m-10) cc_final: 0.6849 (m-80) REVERT: B 334 PHE cc_start: 0.7118 (m-10) cc_final: 0.6672 (m-80) REVERT: C 37 MET cc_start: 0.5982 (tpp) cc_final: 0.5483 (tpp) REVERT: C 75 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7093 (tpp-160) REVERT: C 198 GLN cc_start: 0.7901 (mp-120) cc_final: 0.7143 (mp10) REVERT: C 334 PHE cc_start: 0.7077 (m-10) cc_final: 0.6653 (m-80) REVERT: D 198 GLN cc_start: 0.7189 (mp10) cc_final: 0.6889 (mp10) REVERT: D 334 PHE cc_start: 0.7020 (m-10) cc_final: 0.6647 (m-80) REVERT: F 198 GLN cc_start: 0.7594 (mp-120) cc_final: 0.7002 (mp10) REVERT: G 75 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7191 (tpp-160) REVERT: G 334 PHE cc_start: 0.6998 (m-10) cc_final: 0.6743 (m-80) outliers start: 42 outliers final: 36 residues processed: 255 average time/residue: 0.2399 time to fit residues: 94.1283 Evaluate side-chains 261 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15799 Z= 0.220 Angle : 0.638 9.644 21518 Z= 0.307 Chirality : 0.040 0.127 2653 Planarity : 0.004 0.040 2590 Dihedral : 4.343 58.405 2108 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.09 % Allowed : 18.58 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1946 helix: 1.36 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -1.95 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 104 HIS 0.003 0.001 HIS G 134 PHE 0.013 0.001 PHE E 334 TYR 0.025 0.002 TYR F 121 ARG 0.002 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7184 (m-10) cc_final: 0.6922 (m-80) REVERT: B 334 PHE cc_start: 0.7127 (m-10) cc_final: 0.6732 (m-80) REVERT: C 37 MET cc_start: 0.5684 (tpp) cc_final: 0.5181 (tpp) REVERT: C 75 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7165 (tpp-160) REVERT: C 198 GLN cc_start: 0.7902 (mp-120) cc_final: 0.7139 (mp10) REVERT: C 256 ASP cc_start: 0.7110 (t0) cc_final: 0.6836 (t0) REVERT: C 334 PHE cc_start: 0.7078 (m-10) cc_final: 0.6675 (m-80) REVERT: D 334 PHE cc_start: 0.7122 (m-10) cc_final: 0.6776 (m-80) REVERT: F 198 GLN cc_start: 0.7587 (mp-120) cc_final: 0.7005 (mp10) REVERT: G 75 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7137 (tpp-160) REVERT: G 334 PHE cc_start: 0.7128 (m-10) cc_final: 0.6896 (m-80) outliers start: 51 outliers final: 43 residues processed: 254 average time/residue: 0.2510 time to fit residues: 98.0009 Evaluate side-chains 264 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15799 Z= 0.166 Angle : 0.628 12.234 21518 Z= 0.294 Chirality : 0.039 0.134 2653 Planarity : 0.004 0.040 2590 Dihedral : 4.081 58.135 2108 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.03 % Allowed : 19.49 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1946 helix: 1.69 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 104 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE C 244 TYR 0.025 0.002 TYR A 121 ARG 0.003 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 PHE cc_start: 0.7067 (m-10) cc_final: 0.6675 (m-80) REVERT: C 37 MET cc_start: 0.5735 (tpp) cc_final: 0.5271 (tpp) REVERT: C 75 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7125 (mmm160) REVERT: C 198 GLN cc_start: 0.7676 (mp-120) cc_final: 0.6992 (mp10) REVERT: C 256 ASP cc_start: 0.7124 (t0) cc_final: 0.6748 (t0) REVERT: C 334 PHE cc_start: 0.7046 (m-10) cc_final: 0.6667 (m-80) REVERT: D 198 GLN cc_start: 0.7215 (mp10) cc_final: 0.6804 (mp10) REVERT: D 334 PHE cc_start: 0.7082 (m-10) cc_final: 0.6754 (m-80) REVERT: F 198 GLN cc_start: 0.7523 (mp-120) cc_final: 0.7014 (mp10) REVERT: G 334 PHE cc_start: 0.6930 (m-10) cc_final: 0.6717 (m-80) outliers start: 50 outliers final: 44 residues processed: 253 average time/residue: 0.2480 time to fit residues: 96.8455 Evaluate side-chains 268 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 105 optimal weight: 0.0970 chunk 188 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15799 Z= 0.139 Angle : 0.616 12.230 21518 Z= 0.285 Chirality : 0.038 0.123 2653 Planarity : 0.004 0.040 2590 Dihedral : 3.665 58.242 2104 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.09 % Allowed : 20.34 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1946 helix: 1.77 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.002 0.001 HIS C 217 PHE 0.012 0.001 PHE E 334 TYR 0.025 0.001 TYR A 121 ARG 0.004 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: B 334 PHE cc_start: 0.7014 (m-10) cc_final: 0.6662 (m-80) REVERT: B 352 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7552 (pp20) REVERT: C 37 MET cc_start: 0.5753 (tpp) cc_final: 0.5381 (tpp) REVERT: C 75 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7172 (tpp-160) REVERT: C 198 GLN cc_start: 0.7660 (mp-120) cc_final: 0.6958 (mp10) REVERT: C 224 ILE cc_start: 0.7282 (mm) cc_final: 0.7068 (mt) REVERT: C 334 PHE cc_start: 0.6850 (m-10) cc_final: 0.6494 (m-80) REVERT: D 334 PHE cc_start: 0.6814 (m-10) cc_final: 0.6499 (m-80) REVERT: G 334 PHE cc_start: 0.6895 (m-10) cc_final: 0.6633 (m-80) outliers start: 51 outliers final: 39 residues processed: 262 average time/residue: 0.2732 time to fit residues: 109.1929 Evaluate side-chains 268 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15799 Z= 0.199 Angle : 0.646 11.544 21518 Z= 0.306 Chirality : 0.039 0.122 2653 Planarity : 0.004 0.042 2590 Dihedral : 3.857 58.269 2104 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.78 % Allowed : 21.97 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1946 helix: 1.66 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 104 HIS 0.003 0.001 HIS F 134 PHE 0.012 0.001 PHE C 244 TYR 0.026 0.002 TYR F 121 ARG 0.002 0.000 ARG E 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: B 334 PHE cc_start: 0.7111 (m-10) cc_final: 0.6732 (m-80) REVERT: B 352 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: C 37 MET cc_start: 0.5973 (tpp) cc_final: 0.5556 (tpp) REVERT: C 75 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7061 (tpp80) REVERT: C 198 GLN cc_start: 0.7687 (mp-120) cc_final: 0.6995 (mp10) REVERT: C 256 ASP cc_start: 0.7100 (t0) cc_final: 0.6829 (t0) REVERT: C 334 PHE cc_start: 0.6988 (m-10) cc_final: 0.6611 (m-80) REVERT: D 334 PHE cc_start: 0.7111 (m-10) cc_final: 0.6760 (m-80) REVERT: D 352 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: E 352 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7629 (pp20) REVERT: G 334 PHE cc_start: 0.7061 (m-10) cc_final: 0.6843 (m-80) outliers start: 46 outliers final: 40 residues processed: 238 average time/residue: 0.2487 time to fit residues: 91.5873 Evaluate side-chains 262 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 0.1980 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15799 Z= 0.155 Angle : 0.632 12.299 21518 Z= 0.295 Chirality : 0.038 0.119 2653 Planarity : 0.004 0.041 2590 Dihedral : 3.692 58.105 2104 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.03 % Allowed : 21.85 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1946 helix: 1.72 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 104 HIS 0.002 0.001 HIS G 134 PHE 0.010 0.001 PHE G 244 TYR 0.026 0.001 TYR A 121 ARG 0.002 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: B 224 ILE cc_start: 0.7170 (mm) cc_final: 0.6957 (mt) REVERT: B 334 PHE cc_start: 0.7071 (m-10) cc_final: 0.6698 (m-80) REVERT: B 352 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: C 37 MET cc_start: 0.5820 (tpp) cc_final: 0.5419 (tpp) REVERT: C 75 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7141 (tpp-160) REVERT: C 198 GLN cc_start: 0.7655 (mp-120) cc_final: 0.6802 (mp10) REVERT: C 224 ILE cc_start: 0.7275 (mm) cc_final: 0.7068 (mt) REVERT: C 256 ASP cc_start: 0.7095 (t0) cc_final: 0.6798 (t0) REVERT: C 334 PHE cc_start: 0.6978 (m-10) cc_final: 0.6618 (m-80) REVERT: C 352 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: D 334 PHE cc_start: 0.7077 (m-10) cc_final: 0.6742 (m-80) REVERT: D 352 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: E 352 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (pp20) REVERT: G 334 PHE cc_start: 0.6831 (m-10) cc_final: 0.6569 (m-80) REVERT: G 352 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7543 (pp20) outliers start: 50 outliers final: 40 residues processed: 242 average time/residue: 0.2402 time to fit residues: 90.6749 Evaluate side-chains 264 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15799 Z= 0.192 Angle : 0.654 12.271 21518 Z= 0.308 Chirality : 0.039 0.121 2653 Planarity : 0.004 0.043 2590 Dihedral : 3.832 58.176 2104 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.03 % Allowed : 21.91 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1946 helix: 1.70 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 104 HIS 0.003 0.001 HIS F 134 PHE 0.012 0.001 PHE A 244 TYR 0.028 0.002 TYR A 121 ARG 0.002 0.000 ARG G 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: A 334 PHE cc_start: 0.6911 (m-80) cc_final: 0.6654 (m-80) REVERT: B 334 PHE cc_start: 0.7087 (m-10) cc_final: 0.6714 (m-80) REVERT: B 352 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: C 37 MET cc_start: 0.5838 (tpp) cc_final: 0.5431 (tpp) REVERT: C 75 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7007 (tpp80) REVERT: C 198 GLN cc_start: 0.7696 (mp-120) cc_final: 0.6836 (mp10) REVERT: C 224 ILE cc_start: 0.7283 (mm) cc_final: 0.7075 (mt) REVERT: C 256 ASP cc_start: 0.7187 (t0) cc_final: 0.6879 (t0) REVERT: C 334 PHE cc_start: 0.6982 (m-10) cc_final: 0.6594 (m-80) REVERT: C 352 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7636 (pp20) REVERT: D 334 PHE cc_start: 0.7134 (m-10) cc_final: 0.6790 (m-80) REVERT: D 352 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7170 (pp20) REVERT: E 352 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7686 (pp20) REVERT: G 334 PHE cc_start: 0.6962 (m-10) cc_final: 0.6761 (m-80) REVERT: G 352 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7610 (pp20) outliers start: 50 outliers final: 40 residues processed: 245 average time/residue: 0.2549 time to fit residues: 96.7840 Evaluate side-chains 265 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130494 restraints weight = 20764.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135276 restraints weight = 12509.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138482 restraints weight = 8983.939| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15799 Z= 0.195 Angle : 0.660 12.210 21518 Z= 0.310 Chirality : 0.039 0.121 2653 Planarity : 0.004 0.042 2590 Dihedral : 3.853 57.978 2104 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.91 % Allowed : 22.09 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1946 helix: 1.70 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 104 HIS 0.002 0.001 HIS G 134 PHE 0.012 0.001 PHE A 244 TYR 0.028 0.002 TYR F 121 ARG 0.003 0.000 ARG G 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.70 seconds wall clock time: 53 minutes 36.06 seconds (3216.06 seconds total)