Starting phenix.real_space_refine on Tue Dec 31 15:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtt_34267/12_2024/8gtt_34267_neut.cif" } resolution = 3.2 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= 0.000 sd= 0.031 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 10759 2.51 5 N 2534 2.21 5 O 2877 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: 16247 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2321 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.45, per 1000 atoms: 0.40 Number of scatterers: 16247 At special positions: 0 Unit cell: (106.68, 108.36, 118.44, 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 2877 8.00 N 2534 7.00 C 10759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 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: 3.98 Conformation dependent library (CDL) restraints added in 2.1 seconds 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4130 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 71.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 33 through 54 removed outlier: 4.112A pdb=" N THR A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.901A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.560A pdb=" N ALA A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.331A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 158 Proline residue: A 123 - end of helix Proline residue: A 133 - end of helix removed outlier: 4.254A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.698A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 236 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.752A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 296 Proline residue: A 289 - end of helix removed outlier: 3.948A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.749A pdb=" N GLN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.755A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.757A pdb=" N ASN A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 54 removed outlier: 4.113A pdb=" N THR B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.900A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.560A pdb=" N ALA B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.332A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 158 Proline residue: B 123 - end of helix Proline residue: B 133 - end of helix removed outlier: 4.254A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS B 158 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.698A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 236 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.752A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 296 Proline residue: B 289 - end of helix removed outlier: 3.949A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.749A pdb=" N GLN B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.755A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.757A pdb=" N ASN B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 removed outlier: 4.113A pdb=" N THR C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.901A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.560A pdb=" N ALA C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.331A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 158 Proline residue: C 123 - end of helix Proline residue: C 133 - end of helix removed outlier: 4.254A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.698A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 236 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.752A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 296 Proline residue: C 289 - end of helix removed outlier: 3.948A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.749A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.755A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.757A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 54 removed outlier: 4.112A pdb=" N THR D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.901A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.560A pdb=" N ALA D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 108 removed outlier: 4.331A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 158 Proline residue: D 123 - end of helix Proline residue: D 133 - end of helix removed outlier: 4.253A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS D 158 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.698A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 236 Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.752A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 296 Proline residue: D 289 - end of helix removed outlier: 3.948A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.749A pdb=" N GLN D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.755A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.757A pdb=" N ASN D 369 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 54 removed outlier: 4.112A pdb=" N THR E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.901A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.560A pdb=" N ALA E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 108 removed outlier: 4.332A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 158 Proline residue: E 123 - end of helix Proline residue: E 133 - end of helix removed outlier: 4.254A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.699A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 236 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.751A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 296 Proline residue: E 289 - end of helix removed outlier: 3.948A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.748A pdb=" N GLN E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.756A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN E 338 " --> pdb=" O PHE E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.757A pdb=" N ASN E 369 " --> pdb=" O LEU E 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 54 removed outlier: 4.113A pdb=" N THR F 39 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.901A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.561A pdb=" N ALA F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.332A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 158 Proline residue: F 123 - end of helix Proline residue: F 133 - end of helix removed outlier: 4.254A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.699A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 236 Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.750A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 296 Proline residue: F 289 - end of helix removed outlier: 3.947A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.748A pdb=" N GLN F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.755A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.125A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.755A pdb=" N ASN F 369 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 54 removed outlier: 4.113A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.901A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 87 removed outlier: 3.561A pdb=" N ALA G 78 " --> pdb=" O ARG G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 108 removed outlier: 4.332A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 158 Proline residue: G 123 - end of helix Proline residue: G 133 - end of helix removed outlier: 4.254A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.698A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 236 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.751A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 296 Proline residue: G 289 - end of helix removed outlier: 3.948A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.749A pdb=" N GLN G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.756A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN G 338 " --> pdb=" O PHE G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.124A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.756A pdb=" N ASN G 369 " --> pdb=" O LEU G 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN A 264 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN B 264 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN C 264 " --> pdb=" O PHE C 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN D 264 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN E 264 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN F 264 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.236A pdb=" N GLN G 264 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2961 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: 4.93 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2669 1.32 - 1.45: 4225 1.45 - 1.57: 9612 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 16597 Sorted by residual: bond pdb=" C ASP G 35 " pdb=" O ASP G 35 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.33e-02 5.65e+03 6.22e+00 bond pdb=" C ASP D 35 " pdb=" O ASP D 35 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.33e-02 5.65e+03 5.83e+00 bond pdb=" C ASP C 35 " pdb=" O ASP C 35 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.33e-02 5.65e+03 5.80e+00 bond pdb=" C ASP B 35 " pdb=" O ASP B 35 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.33e-02 5.65e+03 5.79e+00 bond pdb=" C ASP A 35 " pdb=" O ASP A 35 " ideal model delta sigma weight residual 1.235 1.203 0.032 1.33e-02 5.65e+03 5.77e+00 ... (remaining 16592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 22406 2.44 - 4.88: 175 4.88 - 7.32: 36 7.32 - 9.75: 7 9.75 - 12.19: 7 Bond angle restraints: 22631 Sorted by residual: angle pdb=" N LYS C 36 " pdb=" CA LYS C 36 " pdb=" C LYS C 36 " ideal model delta sigma weight residual 114.31 102.12 12.19 1.29e+00 6.01e-01 8.93e+01 angle pdb=" N LYS F 36 " pdb=" CA LYS F 36 " pdb=" C LYS F 36 " ideal model delta sigma weight residual 114.31 102.13 12.18 1.29e+00 6.01e-01 8.92e+01 angle pdb=" N LYS G 36 " pdb=" CA LYS G 36 " pdb=" C LYS G 36 " ideal model delta sigma weight residual 114.31 102.14 12.17 1.29e+00 6.01e-01 8.90e+01 angle pdb=" N LYS A 36 " pdb=" CA LYS A 36 " pdb=" C LYS A 36 " ideal model delta sigma weight residual 114.31 102.14 12.17 1.29e+00 6.01e-01 8.90e+01 angle pdb=" N LYS E 36 " pdb=" CA LYS E 36 " pdb=" C LYS E 36 " ideal model delta sigma weight residual 114.31 102.16 12.15 1.29e+00 6.01e-01 8.87e+01 ... (remaining 22626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.95: 8221 14.95 - 29.89: 1051 29.89 - 44.84: 457 44.84 - 59.79: 147 59.79 - 74.73: 28 Dihedral angle restraints: 9904 sinusoidal: 3576 harmonic: 6328 Sorted by residual: dihedral pdb=" C LYS C 36 " pdb=" N LYS C 36 " pdb=" CA LYS C 36 " pdb=" CB LYS C 36 " ideal model delta harmonic sigma weight residual -122.60 -113.49 -9.11 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C LYS F 36 " pdb=" N LYS F 36 " pdb=" CA LYS F 36 " pdb=" CB LYS F 36 " ideal model delta harmonic sigma weight residual -122.60 -113.56 -9.04 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" C LYS A 36 " pdb=" N LYS A 36 " pdb=" CA LYS A 36 " pdb=" CB LYS A 36 " ideal model delta harmonic sigma weight residual -122.60 -113.57 -9.03 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 9901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2416 0.059 - 0.117: 333 0.117 - 0.176: 9 0.176 - 0.235: 0 0.235 - 0.293: 7 Chirality restraints: 2765 Sorted by residual: chirality pdb=" CA LYS C 36 " pdb=" N LYS C 36 " pdb=" C LYS C 36 " pdb=" CB LYS C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LYS F 36 " pdb=" N LYS F 36 " pdb=" C LYS F 36 " pdb=" CB LYS F 36 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS A 36 " pdb=" N LYS A 36 " pdb=" C LYS A 36 " pdb=" CB LYS A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2762 not shown) Planarity restraints: 2779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO C 124 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 123 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 124 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 123 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.76e+00 pdb=" N PRO A 124 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.028 5.00e-02 4.00e+02 ... (remaining 2776 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 105 2.60 - 3.18: 14216 3.18 - 3.75: 25752 3.75 - 4.33: 32437 4.33 - 4.90: 56898 Nonbonded interactions: 129408 Sorted by model distance: nonbonded pdb=" SG CYS F 66 " pdb=" SG CYS F 265 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 66 " pdb=" SG CYS E 265 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS G 66 " pdb=" SG CYS G 265 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 66 " pdb=" SG CYS D 265 " model vdw 2.029 3.760 ... (remaining 129403 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 33.270 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.033 16597 Z= 0.210 Angle : 0.640 12.193 22631 Z= 0.338 Chirality : 0.042 0.293 2765 Planarity : 0.004 0.049 2779 Dihedral : 17.607 74.733 5768 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.58 % Allowed : 36.26 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.19), residues: 2079 helix: 1.64 (0.15), residues: 1379 sheet: -1.20 (0.54), residues: 84 loop : -1.71 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 104 HIS 0.001 0.000 HIS B 106 PHE 0.008 0.001 PHE D 244 TYR 0.006 0.001 TYR B 331 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 1.765 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 195 average time/residue: 0.3476 time to fit residues: 97.0410 Evaluate side-chains 184 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain G residue 36 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16597 Z= 0.216 Angle : 0.606 11.050 22631 Z= 0.289 Chirality : 0.041 0.124 2765 Planarity : 0.004 0.049 2779 Dihedral : 3.881 17.267 2260 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.15 % Allowed : 30.54 % Favored : 64.31 % 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: 2079 helix: 1.69 (0.15), residues: 1449 sheet: -0.89 (0.58), residues: 84 loop : -1.63 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 104 HIS 0.001 0.000 HIS D 106 PHE 0.011 0.001 PHE G 244 TYR 0.013 0.001 TYR G 331 ARG 0.001 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 180 time to evaluate : 1.975 Fit side-chains outliers start: 89 outliers final: 62 residues processed: 250 average time/residue: 0.2983 time to fit residues: 110.1855 Evaluate side-chains 237 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.7605 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16597 Z= 0.251 Angle : 0.620 11.087 22631 Z= 0.294 Chirality : 0.042 0.124 2765 Planarity : 0.004 0.049 2779 Dihedral : 4.010 17.431 2240 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.21 % Allowed : 32.39 % Favored : 62.41 % 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: 2079 helix: 1.67 (0.15), residues: 1449 sheet: -0.91 (0.59), residues: 84 loop : -1.73 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 104 HIS 0.001 0.001 HIS D 106 PHE 0.013 0.001 PHE B 244 TYR 0.013 0.001 TYR G 331 ARG 0.002 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 178 time to evaluate : 1.698 Fit side-chains REVERT: D 250 SER cc_start: 0.8478 (p) cc_final: 0.8100 (m) outliers start: 90 outliers final: 67 residues processed: 250 average time/residue: 0.3163 time to fit residues: 116.5144 Evaluate side-chains 232 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 165 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 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: 0.7565 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16597 Z= 0.187 Angle : 0.587 11.467 22631 Z= 0.272 Chirality : 0.040 0.121 2765 Planarity : 0.004 0.049 2779 Dihedral : 3.805 17.026 2240 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 33.60 % Favored : 62.41 % 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: 1.23 (0.20), residues: 2079 helix: 1.81 (0.15), residues: 1449 sheet: -0.76 (0.60), residues: 84 loop : -1.68 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 104 HIS 0.001 0.000 HIS A 106 PHE 0.008 0.001 PHE D 244 TYR 0.010 0.001 TYR G 331 ARG 0.001 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 1.943 Fit side-chains REVERT: C 195 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6410 (tp) REVERT: D 240 LEU cc_start: 0.7873 (tp) cc_final: 0.7668 (tp) REVERT: F 195 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6485 (tp) REVERT: G 195 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6428 (tp) outliers start: 69 outliers final: 53 residues processed: 230 average time/residue: 0.3375 time to fit residues: 113.9965 Evaluate side-chains 218 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.0060 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 0.3980 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16597 Z= 0.164 Angle : 0.581 11.322 22631 Z= 0.266 Chirality : 0.039 0.117 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.665 16.429 2240 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.51 % Allowed : 33.66 % Favored : 61.83 % 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: 1.36 (0.20), residues: 2079 helix: 1.90 (0.15), residues: 1449 sheet: -0.66 (0.60), residues: 84 loop : -1.65 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 104 HIS 0.001 0.000 HIS A 106 PHE 0.007 0.001 PHE B 244 TYR 0.009 0.001 TYR G 331 ARG 0.001 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 1.717 Fit side-chains REVERT: C 195 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6452 (tp) REVERT: D 195 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6400 (tp) REVERT: F 195 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6528 (tp) REVERT: G 195 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6396 (tp) outliers start: 78 outliers final: 61 residues processed: 237 average time/residue: 0.3069 time to fit residues: 106.5621 Evaluate side-chains 235 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 0.0050 chunk 203 optimal weight: 0.7980 chunk 168 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 0.0030 chunk 106 optimal weight: 0.9990 overall best weight: 0.3804 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16597 Z= 0.149 Angle : 0.570 11.631 22631 Z= 0.260 Chirality : 0.039 0.121 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.516 15.379 2240 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.93 % Allowed : 34.12 % Favored : 61.94 % 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: 1.46 (0.20), residues: 2079 helix: 1.96 (0.15), residues: 1449 sheet: -0.54 (0.59), residues: 84 loop : -1.56 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.001 0.000 HIS A 106 PHE 0.005 0.001 PHE G 244 TYR 0.010 0.001 TYR B 331 ARG 0.001 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 1.865 Fit side-chains REVERT: A 250 SER cc_start: 0.8339 (p) cc_final: 0.8029 (m) REVERT: B 336 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7129 (mt-10) REVERT: F 233 TYR cc_start: 0.7774 (t80) cc_final: 0.7516 (t80) REVERT: G 336 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7035 (mt-10) outliers start: 68 outliers final: 61 residues processed: 227 average time/residue: 0.3157 time to fit residues: 104.5355 Evaluate side-chains 226 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 0.0970 chunk 148 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16597 Z= 0.162 Angle : 0.583 16.637 22631 Z= 0.263 Chirality : 0.039 0.140 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.503 14.813 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.05 % Allowed : 33.55 % Favored : 62.41 % 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: 1.46 (0.20), residues: 2079 helix: 1.91 (0.15), residues: 1456 sheet: -0.56 (0.59), residues: 84 loop : -1.45 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 104 HIS 0.001 0.000 HIS D 106 PHE 0.008 0.001 PHE B 244 TYR 0.009 0.001 TYR B 331 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 1.831 Fit side-chains REVERT: E 341 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5936 (tt0) REVERT: F 233 TYR cc_start: 0.7816 (t80) cc_final: 0.7518 (t80) REVERT: G 268 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (mm) REVERT: G 336 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7022 (mt-10) outliers start: 70 outliers final: 59 residues processed: 231 average time/residue: 0.3352 time to fit residues: 112.8111 Evaluate side-chains 236 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7539 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16597 Z= 0.173 Angle : 0.591 16.065 22631 Z= 0.268 Chirality : 0.040 0.151 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.540 14.791 2240 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.16 % Allowed : 33.08 % Favored : 62.75 % 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: 1.41 (0.20), residues: 2079 helix: 1.91 (0.15), residues: 1449 sheet: -0.63 (0.59), residues: 84 loop : -1.50 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 104 HIS 0.001 0.000 HIS A 106 PHE 0.009 0.001 PHE E 244 TYR 0.010 0.001 TYR B 331 ARG 0.001 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 188 time to evaluate : 2.092 Fit side-chains REVERT: A 95 GLN cc_start: 0.7036 (mp10) cc_final: 0.6829 (mp10) REVERT: B 336 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7136 (mt-10) REVERT: F 233 TYR cc_start: 0.7868 (t80) cc_final: 0.7533 (t80) REVERT: G 268 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8537 (mm) REVERT: G 336 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7049 (mt-10) outliers start: 72 outliers final: 61 residues processed: 243 average time/residue: 0.3495 time to fit residues: 126.0237 Evaluate side-chains 244 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 113 optimal weight: 0.0010 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16597 Z= 0.183 Angle : 0.597 15.467 22631 Z= 0.272 Chirality : 0.040 0.140 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.570 15.118 2240 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.93 % Allowed : 33.26 % Favored : 62.81 % 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: 1.39 (0.20), residues: 2079 helix: 1.88 (0.15), residues: 1449 sheet: -0.72 (0.59), residues: 84 loop : -1.48 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 104 HIS 0.001 0.000 HIS D 106 PHE 0.025 0.001 PHE A 299 TYR 0.011 0.001 TYR B 331 ARG 0.001 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 1.945 Fit side-chains REVERT: B 228 CYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7543 (m) REVERT: B 336 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7135 (mt-10) REVERT: F 233 TYR cc_start: 0.7921 (t80) cc_final: 0.7549 (t80) REVERT: G 268 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8512 (mm) REVERT: G 336 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7040 (mt-10) outliers start: 68 outliers final: 61 residues processed: 240 average time/residue: 0.3092 time to fit residues: 109.4526 Evaluate side-chains 246 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 166 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16597 Z= 0.191 Angle : 0.605 15.194 22631 Z= 0.275 Chirality : 0.040 0.144 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.586 14.998 2240 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.59 % Allowed : 33.78 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.20), residues: 2079 helix: 1.87 (0.15), residues: 1449 sheet: -0.78 (0.59), residues: 84 loop : -1.49 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 104 HIS 0.001 0.000 HIS D 106 PHE 0.009 0.001 PHE B 244 TYR 0.011 0.001 TYR B 331 ARG 0.001 0.000 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4158 Ramachandran restraints generated. 2079 Oldfield, 0 Emsley, 2079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 1.774 Fit side-chains REVERT: B 228 CYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7540 (m) REVERT: B 233 TYR cc_start: 0.7907 (t80) cc_final: 0.7691 (t80) REVERT: B 336 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7171 (mt-10) REVERT: G 268 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8513 (mm) REVERT: G 336 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7069 (mt-10) outliers start: 62 outliers final: 56 residues processed: 231 average time/residue: 0.3036 time to fit residues: 102.9605 Evaluate side-chains 239 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 181 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 333 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 346 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.216975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.199995 restraints weight = 16526.870| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 0.65 r_work: 0.3967 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16597 Z= 0.207 Angle : 0.614 15.148 22631 Z= 0.281 Chirality : 0.041 0.145 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.671 15.477 2240 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.64 % Allowed : 33.66 % Favored : 62.70 % 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: 1.31 (0.20), residues: 2079 helix: 1.82 (0.15), residues: 1449 sheet: -0.91 (0.59), residues: 84 loop : -1.48 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 104 HIS 0.001 0.000 HIS D 106 PHE 0.021 0.001 PHE A 299 TYR 0.012 0.001 TYR B 331 ARG 0.001 0.000 ARG E 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.75 seconds wall clock time: 61 minutes 11.98 seconds (3671.98 seconds total)