Starting phenix.real_space_refine on Sat May 17 20:32:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtt_34267/05_2025/8gtt_34267_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtt_34267/05_2025/8gtt_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_34267/05_2025/8gtt_34267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtt_34267/05_2025/8gtt_34267.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtt_34267/05_2025/8gtt_34267_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtt_34267/05_2025/8gtt_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-5687/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: 6.50, 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=14, 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 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 2.2 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: 1.61 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: 5.04 Time building geometry restraints manager: 4.93 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: 8233 14.95 - 29.89: 1069 29.89 - 44.84: 463 44.84 - 59.79: 147 59.79 - 74.73: 28 Dihedral angle restraints: 9940 sinusoidal: 3612 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 9937 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: 2.27 - 2.79: 4248 2.79 - 3.32: 16294 3.32 - 3.85: 26765 3.85 - 4.37: 29037 4.37 - 4.90: 53028 Nonbonded interactions: 129372 Sorted by model distance: nonbonded pdb=" OH TYR F 83 " pdb=" OG SER F 250 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR C 83 " pdb=" OG SER C 250 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR G 83 " pdb=" OG SER G 250 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR D 83 " pdb=" OG SER D 250 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR E 83 " pdb=" OG SER E 250 " model vdw 2.268 3.040 ... (remaining 129367 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 34.560 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- 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 16611 Z= 0.165 Angle : 0.640 12.193 22659 Z= 0.338 Chirality : 0.042 0.293 2765 Planarity : 0.004 0.049 2779 Dihedral : 17.607 74.733 5768 Min Nonbonded Distance : 2.267 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 Details of bonding type rmsd hydrogen bonds : bond 0.12490 ( 1015) hydrogen bonds : angle 4.30354 ( 2961) SS BOND : bond 0.00178 ( 14) SS BOND : angle 0.50123 ( 28) covalent geometry : bond 0.00327 (16597) covalent geometry : angle 0.63996 (22631) *********************** 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 : 1.906 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 195 average time/residue: 0.3420 time to fit residues: 95.3161 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 : 1.669 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.218358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.201632 restraints weight = 16598.696| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 0.59 r_work: 0.3997 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.146 Angle : 0.611 11.199 22659 Z= 0.292 Chirality : 0.041 0.124 2765 Planarity : 0.004 0.049 2779 Dihedral : 3.897 16.773 2260 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.55 % Allowed : 30.71 % Favored : 63.74 % 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: 1.06 (0.20), residues: 2079 helix: 1.68 (0.15), residues: 1449 sheet: -1.40 (0.55), residues: 84 loop : -1.64 (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 0.010 0.001 PHE G 244 TYR 0.014 0.001 TYR G 331 ARG 0.002 0.000 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1015) hydrogen bonds : angle 3.52796 ( 2961) SS BOND : bond 0.00330 ( 14) SS BOND : angle 0.46821 ( 28) covalent geometry : bond 0.00338 (16597) covalent geometry : angle 0.61161 (22631) *********************** 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 271 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 175 time to evaluate : 1.591 Fit side-chains REVERT: D 250 SER cc_start: 0.8434 (p) cc_final: 0.8005 (m) REVERT: E 143 MET cc_start: 0.5788 (mmm) cc_final: 0.5439 (mmt) REVERT: E 349 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7396 (mttm) outliers start: 96 outliers final: 62 residues processed: 253 average time/residue: 0.2689 time to fit residues: 100.6916 Evaluate side-chains 234 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 75 ASP 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 211 ILE 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 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 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 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 146 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 140 optimal weight: 0.0670 chunk 166 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.2980 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.222124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.205139 restraints weight = 16413.203| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 0.61 r_work: 0.4084 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16611 Z= 0.116 Angle : 0.579 11.396 22659 Z= 0.270 Chirality : 0.039 0.113 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.639 17.296 2240 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.95 % Allowed : 32.85 % Favored : 64.20 % 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: 1.33 (0.20), residues: 2079 helix: 1.90 (0.15), residues: 1449 sheet: -1.03 (0.57), residues: 84 loop : -1.64 (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 0.005 0.001 PHE C 263 TYR 0.012 0.001 TYR E 345 ARG 0.001 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 1015) hydrogen bonds : angle 3.26846 ( 2961) SS BOND : bond 0.00215 ( 14) SS BOND : angle 0.54877 ( 28) covalent geometry : bond 0.00246 (16597) covalent geometry : angle 0.57890 (22631) *********************** 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 238 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 1.660 Fit side-chains REVERT: B 47 LEU cc_start: 0.8576 (mm) cc_final: 0.8250 (mm) REVERT: B 240 LEU cc_start: 0.7654 (tp) cc_final: 0.7452 (tp) REVERT: D 149 VAL cc_start: 0.6860 (t) cc_final: 0.6640 (p) outliers start: 51 outliers final: 41 residues processed: 228 average time/residue: 0.2859 time to fit residues: 95.5370 Evaluate side-chains 214 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 195 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU 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 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 195 ILE Chi-restraints excluded: chain E residue 219 LEU 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 219 LEU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 219 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 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 124 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.221346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.203432 restraints weight = 16527.214| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 0.64 r_work: 0.4055 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.116 Angle : 0.579 11.410 22659 Z= 0.268 Chirality : 0.039 0.117 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.578 15.870 2240 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.64 % Allowed : 32.39 % Favored : 63.97 % 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: 1.40 (0.20), residues: 2079 helix: 1.94 (0.15), residues: 1449 sheet: -0.91 (0.58), residues: 84 loop : -1.60 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 104 HIS 0.001 0.000 HIS A 106 PHE 0.007 0.001 PHE D 244 TYR 0.016 0.001 TYR E 345 ARG 0.001 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03082 ( 1015) hydrogen bonds : angle 3.23137 ( 2961) SS BOND : bond 0.00202 ( 14) SS BOND : angle 0.55873 ( 28) covalent geometry : bond 0.00260 (16597) covalent geometry : angle 0.57881 (22631) *********************** 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 243 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 1.770 Fit side-chains REVERT: B 31 GLU cc_start: 0.6116 (tp30) cc_final: 0.5897 (tp30) REVERT: G 195 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6518 (tp) outliers start: 63 outliers final: 57 residues processed: 228 average time/residue: 0.3019 time to fit residues: 100.5290 Evaluate side-chains 223 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.956 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 219 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 96 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 184 optimal weight: 0.0770 chunk 79 optimal weight: 0.0670 chunk 209 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.223360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.206860 restraints weight = 16699.192| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 0.59 r_work: 0.4091 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16611 Z= 0.107 Angle : 0.576 15.453 22659 Z= 0.262 Chirality : 0.039 0.144 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.469 15.215 2240 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.53 % Allowed : 33.08 % Favored : 63.39 % 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: 1.50 (0.20), residues: 2079 helix: 1.97 (0.15), residues: 1456 sheet: -0.82 (0.58), residues: 84 loop : -1.46 (0.28), residues: 539 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 F 244 TYR 0.019 0.001 TYR F 121 ARG 0.001 0.000 ARG B 300 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 1015) hydrogen bonds : angle 3.13301 ( 2961) SS BOND : bond 0.00155 ( 14) SS BOND : angle 0.53745 ( 28) covalent geometry : bond 0.00233 (16597) covalent geometry : angle 0.57647 (22631) *********************** 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 247 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 1.931 Fit side-chains REVERT: E 345 TYR cc_start: 0.7317 (t80) cc_final: 0.6981 (t80) REVERT: E 349 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7302 (mttp) REVERT: F 233 TYR cc_start: 0.7728 (t80) cc_final: 0.7502 (t80) REVERT: G 195 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6466 (tp) outliers start: 61 outliers final: 49 residues processed: 231 average time/residue: 0.3121 time to fit residues: 105.6089 Evaluate side-chains 232 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 195 ILE Chi-restraints excluded: chain F residue 199 TYR 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 219 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 147 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 208 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 186 optimal weight: 0.0030 chunk 134 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.218782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.201204 restraints weight = 16617.965| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 0.64 r_work: 0.4064 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.115 Angle : 0.583 15.862 22659 Z= 0.267 Chirality : 0.039 0.130 2765 Planarity : 0.004 0.044 2779 Dihedral : 3.479 14.893 2240 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.11 % Allowed : 32.74 % 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: 1.45 (0.20), residues: 2079 helix: 1.93 (0.15), residues: 1456 sheet: -0.92 (0.57), residues: 84 loop : -1.45 (0.28), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 104 HIS 0.001 0.000 HIS D 106 PHE 0.008 0.001 PHE D 244 TYR 0.012 0.001 TYR E 345 ARG 0.001 0.000 ARG E 74 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 1015) hydrogen bonds : angle 3.15878 ( 2961) SS BOND : bond 0.00193 ( 14) SS BOND : angle 0.57288 ( 28) covalent geometry : bond 0.00259 (16597) covalent geometry : angle 0.58306 (22631) *********************** 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 262 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 191 time to evaluate : 1.704 Fit side-chains REVERT: D 307 LYS cc_start: 0.8270 (ptmm) cc_final: 0.8055 (ptpt) REVERT: F 233 TYR cc_start: 0.7794 (t80) cc_final: 0.7503 (t80) REVERT: F 307 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8256 (ptpt) outliers start: 71 outliers final: 57 residues processed: 244 average time/residue: 0.2946 time to fit residues: 105.7653 Evaluate side-chains 235 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 B residue 34 VAL Chi-restraints excluded: chain B residue 62 THR 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 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 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 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 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER 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 335 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 181 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 124 optimal weight: 0.0870 chunk 185 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 199 optimal weight: 0.0670 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.220926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.204833 restraints weight = 16489.822| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 0.61 r_work: 0.4011 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16611 Z= 0.110 Angle : 0.582 14.836 22659 Z= 0.265 Chirality : 0.039 0.130 2765 Planarity : 0.004 0.044 2779 Dihedral : 3.442 14.361 2240 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.93 % Allowed : 33.43 % 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: 1.48 (0.20), residues: 2079 helix: 1.93 (0.15), residues: 1456 sheet: -0.84 (0.57), residues: 84 loop : -1.41 (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 A 106 PHE 0.006 0.001 PHE A 244 TYR 0.011 0.001 TYR E 345 ARG 0.001 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 1015) hydrogen bonds : angle 3.13961 ( 2961) SS BOND : bond 0.00176 ( 14) SS BOND : angle 0.52499 ( 28) covalent geometry : bond 0.00245 (16597) covalent geometry : angle 0.58202 (22631) *********************** 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 260 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 192 time to evaluate : 1.626 Fit side-chains REVERT: B 228 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7377 (m) REVERT: D 307 LYS cc_start: 0.8278 (ptmm) cc_final: 0.8056 (ptpt) REVERT: E 345 TYR cc_start: 0.7321 (t80) cc_final: 0.6287 (t80) REVERT: F 233 TYR cc_start: 0.7813 (t80) cc_final: 0.7512 (t80) REVERT: G 268 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8306 (mm) outliers start: 68 outliers final: 54 residues processed: 242 average time/residue: 0.2881 time to fit residues: 102.8308 Evaluate side-chains 239 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.762 ------------------------------------------------------------------------------- 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 62 THR 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 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 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 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 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 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER 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 335 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 144 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4338 r_free = 0.4338 target = 0.214787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.196056 restraints weight = 16656.696| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 0.65 r_work: 0.3921 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16611 Z= 0.167 Angle : 0.645 15.458 22659 Z= 0.299 Chirality : 0.042 0.141 2765 Planarity : 0.004 0.044 2779 Dihedral : 3.786 15.336 2240 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.64 % Allowed : 33.72 % 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: 1.15 (0.20), residues: 2079 helix: 1.71 (0.15), residues: 1449 sheet: -1.29 (0.58), residues: 84 loop : -1.51 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 85 HIS 0.002 0.001 HIS D 106 PHE 0.013 0.001 PHE E 244 TYR 0.015 0.001 TYR B 331 ARG 0.009 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 1015) hydrogen bonds : angle 3.40020 ( 2961) SS BOND : bond 0.00376 ( 14) SS BOND : angle 0.51289 ( 28) covalent geometry : bond 0.00402 (16597) covalent geometry : angle 0.64510 (22631) *********************** 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 254 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 1.706 Fit side-chains REVERT: A 95 GLN cc_start: 0.6931 (mp10) cc_final: 0.6531 (mp-120) REVERT: B 228 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7410 (m) REVERT: B 307 LYS cc_start: 0.8420 (ptmm) cc_final: 0.8092 (ptpt) REVERT: D 250 SER cc_start: 0.8269 (p) cc_final: 0.7902 (m) REVERT: D 307 LYS cc_start: 0.8380 (ptmm) cc_final: 0.8172 (ptpt) REVERT: E 345 TYR cc_start: 0.7496 (t80) cc_final: 0.6505 (t80) REVERT: G 268 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8361 (mm) REVERT: G 307 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8309 (ptpt) outliers start: 63 outliers final: 53 residues processed: 237 average time/residue: 0.2894 time to fit residues: 100.8668 Evaluate side-chains 239 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 62 THR 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 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 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 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 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 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER 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 268 ILE 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 4 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.217090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198829 restraints weight = 16541.271| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 0.68 r_work: 0.3942 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.130 Angle : 0.616 15.726 22659 Z= 0.282 Chirality : 0.040 0.142 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.691 15.374 2240 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.30 % Allowed : 34.30 % 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: 1.20 (0.20), residues: 2079 helix: 1.75 (0.15), residues: 1449 sheet: -1.29 (0.58), residues: 84 loop : -1.50 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 104 HIS 0.001 0.000 HIS G 106 PHE 0.026 0.001 PHE A 299 TYR 0.012 0.001 TYR B 331 ARG 0.001 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 1015) hydrogen bonds : angle 3.29702 ( 2961) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.46822 ( 28) covalent geometry : bond 0.00303 (16597) covalent geometry : angle 0.61605 (22631) *********************** 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 255 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 198 time to evaluate : 1.846 Fit side-chains REVERT: A 95 GLN cc_start: 0.6936 (mp10) cc_final: 0.6527 (mp10) REVERT: B 228 CYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7403 (m) REVERT: B 307 LYS cc_start: 0.8442 (ptmm) cc_final: 0.8202 (ptpt) REVERT: B 336 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7318 (mt-10) REVERT: E 345 TYR cc_start: 0.7366 (t80) cc_final: 0.6792 (t80) REVERT: E 349 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7042 (mmtt) REVERT: F 233 TYR cc_start: 0.7930 (t80) cc_final: 0.7572 (t80) REVERT: G 268 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8299 (mm) REVERT: G 307 LYS cc_start: 0.8560 (ptmm) cc_final: 0.8290 (ptpt) REVERT: G 336 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7249 (mt-10) outliers start: 57 outliers final: 52 residues processed: 239 average time/residue: 0.2847 time to fit residues: 99.9221 Evaluate side-chains 246 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 62 THR 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 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 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 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 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 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER 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 268 ILE 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 183 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 196 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4364 r_free = 0.4364 target = 0.217998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.201140 restraints weight = 16657.696| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 0.64 r_work: 0.3965 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.123 Angle : 0.612 16.125 22659 Z= 0.278 Chirality : 0.040 0.140 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.581 14.935 2240 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.12 % Allowed : 34.30 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.20), residues: 2079 helix: 1.81 (0.15), residues: 1449 sheet: -1.17 (0.57), residues: 84 loop : -1.49 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 104 HIS 0.001 0.000 HIS D 106 PHE 0.008 0.001 PHE E 244 TYR 0.011 0.001 TYR B 331 ARG 0.003 0.000 ARG B 217 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 1015) hydrogen bonds : angle 3.25579 ( 2961) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.48719 ( 28) covalent geometry : bond 0.00284 (16597) covalent geometry : angle 0.61230 (22631) ********************** 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 240 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 1.852 Fit side-chains REVERT: A 95 GLN cc_start: 0.6904 (mp10) cc_final: 0.6471 (mp-120) REVERT: B 228 CYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7429 (m) REVERT: B 336 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 138 ASP cc_start: 0.6837 (m-30) cc_final: 0.6584 (m-30) REVERT: F 233 TYR cc_start: 0.7982 (t80) cc_final: 0.7653 (t80) REVERT: G 268 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8298 (mm) REVERT: G 307 LYS cc_start: 0.8521 (ptmm) cc_final: 0.8275 (ptpt) REVERT: G 336 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7423 (mt-10) outliers start: 54 outliers final: 49 residues processed: 222 average time/residue: 0.3006 time to fit residues: 97.7754 Evaluate side-chains 234 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 62 THR 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 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 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 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 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 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 199 TYR 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 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 83 optimal weight: 0.0060 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.218463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.201536 restraints weight = 16545.253| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 0.64 r_work: 0.3974 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16611 Z= 0.117 Angle : 0.606 15.866 22659 Z= 0.275 Chirality : 0.040 0.140 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.537 14.795 2240 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.01 % Allowed : 34.36 % 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: 1.88 (0.15), residues: 1449 sheet: -1.06 (0.57), residues: 84 loop : -1.46 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 104 HIS 0.001 0.000 HIS A 106 PHE 0.007 0.001 PHE G 244 TYR 0.011 0.001 TYR B 331 ARG 0.001 0.000 ARG G 217 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 1015) hydrogen bonds : angle 3.21677 ( 2961) SS BOND : bond 0.00185 ( 14) SS BOND : angle 0.48923 ( 28) covalent geometry : bond 0.00266 (16597) covalent geometry : angle 0.60573 (22631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7660.97 seconds wall clock time: 134 minutes 10.84 seconds (8050.84 seconds total)