Starting phenix.real_space_refine on Sun Aug 24 01:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtt_34267/08_2025/8gtt_34267_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtt_34267/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gtt_34267/08_2025/8gtt_34267_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtt_34267/08_2025/8gtt_34267_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gtt_34267/08_2025/8gtt_34267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtt_34267/08_2025/8gtt_34267.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 46 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.91, per 1000 atoms: 0.12 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 B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 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: 1.07 Conformation dependent library (CDL) restraints added in 559.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.30 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: 2.21 Time building geometry restraints manager: 1.55 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 74 TYR 0.006 0.001 TYR B 331 PHE 0.008 0.001 PHE D 244 TRP 0.010 0.002 TRP G 104 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00327 (16597) covalent geometry : angle 0.63996 (22631) SS BOND : bond 0.00178 ( 14) SS BOND : angle 0.50123 ( 28) hydrogen bonds : bond 0.12490 ( 1015) hydrogen bonds : angle 4.30354 ( 2961) *********************** 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 : 0.416 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 195 average time/residue: 0.1257 time to fit residues: 35.1042 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 : 0.456 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.222955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.204577 restraints weight = 16651.999| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 0.68 r_work: 0.3991 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16611 Z= 0.129 Angle : 0.592 11.266 22659 Z= 0.281 Chirality : 0.040 0.120 2765 Planarity : 0.004 0.048 2779 Dihedral : 3.778 16.534 2260 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.57 % Allowed : 31.41 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 2079 helix: 1.77 (0.15), residues: 1449 sheet: -1.28 (0.55), residues: 84 loop : -1.60 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 74 TYR 0.011 0.001 TYR G 331 PHE 0.008 0.001 PHE G 244 TRP 0.012 0.002 TRP A 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00287 (16597) covalent geometry : angle 0.59202 (22631) SS BOND : bond 0.00239 ( 14) SS BOND : angle 0.37161 ( 28) hydrogen bonds : bond 0.03653 ( 1015) hydrogen bonds : angle 3.44483 ( 2961) *********************** 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 254 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 175 time to evaluate : 0.554 Fit side-chains REVERT: D 240 LEU cc_start: 0.7701 (tp) cc_final: 0.7483 (tp) REVERT: E 143 MET cc_start: 0.5731 (mmm) cc_final: 0.5425 (mmt) outliers start: 79 outliers final: 53 residues processed: 237 average time/residue: 0.1252 time to fit residues: 43.8846 Evaluate side-chains 224 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 75 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 209 LEU 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 195 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 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 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 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 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 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 7 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 49 optimal weight: 0.0060 chunk 86 optimal weight: 5.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.221423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.204807 restraints weight = 16778.572| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 0.60 r_work: 0.4075 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16611 Z= 0.117 Angle : 0.576 11.341 22659 Z= 0.270 Chirality : 0.039 0.116 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.644 16.493 2240 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.88 % Allowed : 31.69 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 2079 helix: 1.88 (0.15), residues: 1449 sheet: -0.95 (0.57), residues: 84 loop : -1.62 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.010 0.001 TYR G 331 PHE 0.006 0.001 PHE G 244 TRP 0.012 0.002 TRP A 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00259 (16597) covalent geometry : angle 0.57643 (22631) SS BOND : bond 0.00226 ( 14) SS BOND : angle 0.56299 ( 28) hydrogen bonds : bond 0.03258 ( 1015) hydrogen bonds : angle 3.28081 ( 2961) *********************** 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 243 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 176 time to evaluate : 0.512 Fit side-chains REVERT: B 47 LEU cc_start: 0.8575 (mm) cc_final: 0.8242 (mm) REVERT: B 143 MET cc_start: 0.5514 (mmm) cc_final: 0.5202 (mmt) REVERT: B 240 LEU cc_start: 0.7604 (tp) cc_final: 0.7342 (tp) REVERT: D 240 LEU cc_start: 0.7736 (tp) cc_final: 0.7489 (tp) outliers start: 67 outliers final: 51 residues processed: 223 average time/residue: 0.1211 time to fit residues: 40.1020 Evaluate side-chains 216 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 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 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 123 optimal weight: 0.0770 chunk 144 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.220387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.202579 restraints weight = 16566.948| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 0.65 r_work: 0.4037 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16611 Z= 0.123 Angle : 0.592 11.315 22659 Z= 0.273 Chirality : 0.040 0.119 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.627 15.907 2240 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.05 % Allowed : 32.10 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 2079 helix: 1.91 (0.15), residues: 1449 sheet: -1.00 (0.57), residues: 84 loop : -1.61 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.010 0.001 TYR G 331 PHE 0.009 0.001 PHE D 244 TRP 0.011 0.002 TRP A 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00284 (16597) covalent geometry : angle 0.59174 (22631) SS BOND : bond 0.00231 ( 14) SS BOND : angle 0.52857 ( 28) hydrogen bonds : bond 0.03173 ( 1015) hydrogen bonds : angle 3.26366 ( 2961) *********************** 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 249 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 0.646 Fit side-chains REVERT: B 240 LEU cc_start: 0.7653 (tp) cc_final: 0.7419 (tp) REVERT: D 240 LEU cc_start: 0.7738 (tp) cc_final: 0.7476 (tp) outliers start: 70 outliers final: 61 residues processed: 231 average time/residue: 0.1383 time to fit residues: 47.0562 Evaluate side-chains 229 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 88 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain C residue 351 LEU 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 219 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 285 VAL 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 95 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.218188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.199779 restraints weight = 16524.198| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 0.65 r_work: 0.3945 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16611 Z= 0.126 Angle : 0.589 11.716 22659 Z= 0.272 Chirality : 0.040 0.117 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.665 15.791 2240 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.28 % Allowed : 32.62 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.20), residues: 2079 helix: 1.88 (0.15), residues: 1449 sheet: -1.04 (0.57), residues: 84 loop : -1.58 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.010 0.001 TYR G 331 PHE 0.008 0.001 PHE G 244 TRP 0.011 0.002 TRP A 104 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00292 (16597) covalent geometry : angle 0.58900 (22631) SS BOND : bond 0.00266 ( 14) SS BOND : angle 0.52919 ( 28) hydrogen bonds : bond 0.03182 ( 1015) hydrogen bonds : angle 3.25637 ( 2961) *********************** 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 259 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 185 time to evaluate : 0.576 Fit side-chains REVERT: B 240 LEU cc_start: 0.7679 (tp) cc_final: 0.7417 (tp) REVERT: D 240 LEU cc_start: 0.7776 (tp) cc_final: 0.7535 (tp) REVERT: D 307 LYS cc_start: 0.8300 (ptmm) cc_final: 0.8069 (ptpt) REVERT: F 233 TYR cc_start: 0.7849 (t80) cc_final: 0.7538 (t80) REVERT: F 307 LYS cc_start: 0.8612 (ptmm) cc_final: 0.8280 (ptpt) outliers start: 74 outliers final: 63 residues processed: 242 average time/residue: 0.1229 time to fit residues: 43.7316 Evaluate side-chains 241 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 195 ILE 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 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 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 88 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 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 195 ILE Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 239 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.216525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.198035 restraints weight = 16610.995| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 0.66 r_work: 0.3925 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16611 Z= 0.139 Angle : 0.601 11.021 22659 Z= 0.279 Chirality : 0.041 0.126 2765 Planarity : 0.004 0.045 2779 Dihedral : 3.734 15.840 2240 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.68 % Allowed : 33.08 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.20), residues: 2079 helix: 1.81 (0.15), residues: 1449 sheet: -1.19 (0.57), residues: 84 loop : -1.57 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.013 0.001 TYR B 331 PHE 0.010 0.001 PHE B 244 TRP 0.011 0.002 TRP F 85 HIS 0.001 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00330 (16597) covalent geometry : angle 0.60141 (22631) SS BOND : bond 0.00290 ( 14) SS BOND : angle 0.51940 ( 28) hydrogen bonds : bond 0.03311 ( 1015) hydrogen bonds : angle 3.32138 ( 2961) *********************** 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 272 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 191 time to evaluate : 0.606 Fit side-chains REVERT: A 95 GLN cc_start: 0.6940 (mp10) cc_final: 0.6480 (mp10) REVERT: B 240 LEU cc_start: 0.7676 (tp) cc_final: 0.7417 (tp) REVERT: D 240 LEU cc_start: 0.7808 (tp) cc_final: 0.7583 (tp) REVERT: D 307 LYS cc_start: 0.8345 (ptmm) cc_final: 0.8093 (ptpt) REVERT: E 138 ASP cc_start: 0.6589 (m-30) cc_final: 0.6374 (m-30) REVERT: E 307 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8292 (ptpt) REVERT: F 307 LYS cc_start: 0.8647 (ptmm) cc_final: 0.8397 (ptpt) REVERT: G 268 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8335 (mm) REVERT: G 336 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7194 (mt-10) outliers start: 81 outliers final: 59 residues processed: 254 average time/residue: 0.1210 time to fit residues: 45.7661 Evaluate side-chains 242 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 73 SER 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 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS 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 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 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 341 GLU Chi-restraints excluded: chain E residue 346 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 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 285 VAL 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 123 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 139 optimal weight: 0.3980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.211916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.194173 restraints weight = 16563.727| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 0.66 r_work: 0.3883 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16611 Z= 0.198 Angle : 0.673 11.385 22659 Z= 0.317 Chirality : 0.044 0.168 2765 Planarity : 0.004 0.046 2779 Dihedral : 4.173 17.430 2240 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.57 % Allowed : 33.14 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.20), residues: 2079 helix: 1.46 (0.14), residues: 1449 sheet: -1.46 (0.60), residues: 84 loop : -1.62 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 29 TYR 0.025 0.001 TYR G 121 PHE 0.016 0.001 PHE E 244 TRP 0.016 0.003 TRP F 85 HIS 0.002 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00483 (16597) covalent geometry : angle 0.67303 (22631) SS BOND : bond 0.00493 ( 14) SS BOND : angle 0.54399 ( 28) hydrogen bonds : bond 0.04046 ( 1015) hydrogen bonds : angle 3.63572 ( 2961) *********************** 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 282 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 0.568 Fit side-chains REVERT: A 95 GLN cc_start: 0.6954 (mp10) cc_final: 0.6562 (mp-120) REVERT: B 336 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7371 (mt-10) REVERT: D 250 SER cc_start: 0.8322 (p) cc_final: 0.7966 (m) REVERT: G 268 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8380 (mm) REVERT: G 307 LYS cc_start: 0.8626 (ptmm) cc_final: 0.8359 (ptpt) REVERT: G 336 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7480 (mt-10) outliers start: 79 outliers final: 67 residues processed: 261 average time/residue: 0.1208 time to fit residues: 46.9705 Evaluate side-chains 261 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 149 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 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 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 73 SER Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 149 VAL 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 73 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 115 LEU 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 285 VAL 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: 10.0000 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 154 optimal weight: 0.0570 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 196 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.216138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.197765 restraints weight = 16642.924| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 0.68 r_work: 0.3920 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2170 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= 0.122 Angle : 0.598 11.219 22659 Z= 0.277 Chirality : 0.040 0.137 2765 Planarity : 0.004 0.046 2779 Dihedral : 3.823 16.686 2240 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.93 % Allowed : 34.30 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.20), residues: 2079 helix: 1.70 (0.15), residues: 1449 sheet: -1.37 (0.59), residues: 84 loop : -1.56 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.017 0.001 TYR G 121 PHE 0.025 0.001 PHE A 299 TRP 0.014 0.002 TRP F 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00280 (16597) covalent geometry : angle 0.59816 (22631) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.53547 ( 28) hydrogen bonds : bond 0.03214 ( 1015) hydrogen bonds : angle 3.34058 ( 2961) *********************** 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 271 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 0.500 Fit side-chains REVERT: A 95 GLN cc_start: 0.6966 (mp10) cc_final: 0.6539 (mp10) REVERT: A 250 SER cc_start: 0.8253 (p) cc_final: 0.7904 (m) REVERT: B 228 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7447 (m) REVERT: B 307 LYS cc_start: 0.8439 (ptmm) cc_final: 0.8212 (ptpt) REVERT: B 336 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 250 SER cc_start: 0.8232 (p) cc_final: 0.7879 (m) REVERT: D 268 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8182 (mm) REVERT: F 250 SER cc_start: 0.8176 (p) cc_final: 0.7802 (m) REVERT: G 268 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8280 (mm) REVERT: G 307 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8326 (ptpt) REVERT: G 336 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7488 (mt-10) outliers start: 68 outliers final: 58 residues processed: 253 average time/residue: 0.1175 time to fit residues: 44.3552 Evaluate side-chains 258 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 197 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 199 TYR 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 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 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 277 SER 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 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 268 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 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 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 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 109 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 183 optimal weight: 0.0570 chunk 20 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.214830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.196843 restraints weight = 16523.008| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 0.68 r_work: 0.3904 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16611 Z= 0.144 Angle : 0.618 10.961 22659 Z= 0.286 Chirality : 0.041 0.141 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.853 16.573 2240 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.82 % Allowed : 34.36 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.20), residues: 2079 helix: 1.67 (0.15), residues: 1449 sheet: -1.40 (0.59), residues: 84 loop : -1.58 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.011 0.001 TYR B 331 PHE 0.010 0.001 PHE D 244 TRP 0.011 0.002 TRP F 85 HIS 0.002 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00345 (16597) covalent geometry : angle 0.61798 (22631) SS BOND : bond 0.00313 ( 14) SS BOND : angle 0.56589 ( 28) hydrogen bonds : bond 0.03391 ( 1015) hydrogen bonds : angle 3.38400 ( 2961) *********************** 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 265 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 0.499 Fit side-chains REVERT: B 336 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7378 (mt-10) REVERT: D 250 SER cc_start: 0.8266 (p) cc_final: 0.7908 (m) REVERT: D 268 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8252 (mm) REVERT: F 250 SER cc_start: 0.8202 (p) cc_final: 0.7844 (m) REVERT: G 138 ASP cc_start: 0.6783 (m-30) cc_final: 0.6574 (m-30) REVERT: G 268 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8334 (mm) REVERT: G 307 LYS cc_start: 0.8634 (ptmm) cc_final: 0.8393 (ptpt) REVERT: G 336 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7426 (mt-10) outliers start: 66 outliers final: 57 residues processed: 247 average time/residue: 0.1166 time to fit residues: 43.0112 Evaluate side-chains 254 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 199 TYR 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 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER 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 88 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 199 TYR 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 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 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 285 VAL 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 137 optimal weight: 0.3980 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 201 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 = 0.4344 r_free = 0.4344 target = 0.215836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.197603 restraints weight = 16515.550| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 0.69 r_work: 0.3917 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2378 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= 0.134 Angle : 0.609 10.995 22659 Z= 0.281 Chirality : 0.041 0.140 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.775 16.379 2240 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.47 % Allowed : 34.70 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.20), residues: 2079 helix: 1.71 (0.15), residues: 1449 sheet: -1.36 (0.59), residues: 84 loop : -1.57 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 300 TYR 0.010 0.001 TYR B 331 PHE 0.009 0.001 PHE B 244 TRP 0.013 0.002 TRP F 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00316 (16597) covalent geometry : angle 0.60920 (22631) SS BOND : bond 0.00284 ( 14) SS BOND : angle 0.54585 ( 28) hydrogen bonds : bond 0.03239 ( 1015) hydrogen bonds : angle 3.33643 ( 2961) ********************** 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 258 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.699 Fit side-chains REVERT: B 138 ASP cc_start: 0.6710 (m-30) cc_final: 0.6450 (m-30) REVERT: B 228 CYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7482 (m) REVERT: B 336 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 138 ASP cc_start: 0.6869 (m-30) cc_final: 0.6619 (m-30) REVERT: D 250 SER cc_start: 0.8247 (p) cc_final: 0.7897 (m) REVERT: D 268 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (mm) REVERT: F 250 SER cc_start: 0.8188 (p) cc_final: 0.7833 (m) REVERT: G 138 ASP cc_start: 0.6817 (m-30) cc_final: 0.6613 (m-30) REVERT: G 268 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8317 (mm) REVERT: G 307 LYS cc_start: 0.8646 (ptmm) cc_final: 0.8435 (ptpt) REVERT: G 336 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7457 (mt-10) outliers start: 60 outliers final: 53 residues processed: 240 average time/residue: 0.1266 time to fit residues: 45.1518 Evaluate side-chains 252 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 199 TYR 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 199 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 346 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 199 TYR 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 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 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 17 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 67 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 189 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 66 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 overall best weight: 0.8634 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.215363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.198059 restraints weight = 16495.946| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 0.65 r_work: 0.3941 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16611 Z= 0.136 Angle : 0.613 10.894 22659 Z= 0.282 Chirality : 0.041 0.140 2765 Planarity : 0.004 0.047 2779 Dihedral : 3.761 16.054 2240 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.76 % Allowed : 34.64 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.20), residues: 2079 helix: 1.73 (0.15), residues: 1449 sheet: -1.36 (0.59), residues: 84 loop : -1.55 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.010 0.001 TYR B 331 PHE 0.011 0.001 PHE A 116 TRP 0.012 0.002 TRP F 104 HIS 0.001 0.000 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00321 (16597) covalent geometry : angle 0.61351 (22631) SS BOND : bond 0.00286 ( 14) SS BOND : angle 0.54552 ( 28) hydrogen bonds : bond 0.03267 ( 1015) hydrogen bonds : angle 3.33825 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3356.90 seconds wall clock time: 58 minutes 16.82 seconds (3496.82 seconds total)