Starting phenix.real_space_refine on Thu Jul 2 08:20:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sip_25147/07_2026/7sip_25147.map" } resolution = 3.0 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= -0.001 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 4 5.49 5 S 36 5.16 5 C 5192 2.51 5 N 1096 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7560 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1747 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 165 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 4 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 137 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.41, per 1000 atoms: 0.19 Number of scatterers: 7560 At special positions: 0 Unit cell: (98.04, 97.18, 65.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 4 15.00 O 1228 8.00 N 1096 7.00 C 5192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 249.4 milliseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 84.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.896A pdb=" N LEU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.705A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 232 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 6.051A pdb=" N GLU A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 removed outlier: 3.826A pdb=" N VAL A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.518A pdb=" N THR A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.558A pdb=" N ARG A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 392 through 417 removed outlier: 4.018A pdb=" N SER A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.531A pdb=" N THR A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 removed outlier: 3.704A pdb=" N ILE A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 4.203A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 247 removed outlier: 3.706A pdb=" N VAL B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 247 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 6.051A pdb=" N GLU B 251 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 329 removed outlier: 3.826A pdb=" N VAL B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Proline residue: B 322 - end of helix removed outlier: 3.518A pdb=" N THR B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 368 through 378 removed outlier: 3.558A pdb=" N ARG B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 391 Processing helix chain 'B' and resid 392 through 417 removed outlier: 4.018A pdb=" N SER B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.532A pdb=" N THR B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 removed outlier: 3.704A pdb=" N ILE B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 489 removed outlier: 4.204A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 247 removed outlier: 3.705A pdb=" N VAL C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 247 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 253 removed outlier: 6.050A pdb=" N GLU C 251 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 329 removed outlier: 3.826A pdb=" N VAL C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.518A pdb=" N THR C 326 " --> pdb=" O PRO C 322 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 367 Processing helix chain 'C' and resid 368 through 378 removed outlier: 3.558A pdb=" N ARG C 377 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 392 through 417 removed outlier: 4.018A pdb=" N SER C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 414 " --> pdb=" O PHE C 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 removed outlier: 3.531A pdb=" N THR C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 removed outlier: 3.704A pdb=" N ILE C 464 " --> pdb=" O SER C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 489 removed outlier: 4.204A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 247 removed outlier: 3.705A pdb=" N VAL D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 247 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 253 removed outlier: 6.051A pdb=" N GLU D 251 " --> pdb=" O THR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.859A pdb=" N LEU D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 329 removed outlier: 3.826A pdb=" N VAL D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.518A pdb=" N THR D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 368 through 378 removed outlier: 3.558A pdb=" N ARG D 377 " --> pdb=" O LYS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 391 Processing helix chain 'D' and resid 392 through 417 removed outlier: 4.018A pdb=" N SER D 412 " --> pdb=" O VAL D 408 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 414 " --> pdb=" O PHE D 410 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.532A pdb=" N THR D 441 " --> pdb=" O VAL D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 removed outlier: 3.703A pdb=" N ILE D 464 " --> pdb=" O SER D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 489 removed outlier: 4.204A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1272 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: 0.68 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1032 1.31 - 1.44: 2108 1.44 - 1.56: 4364 1.56 - 1.68: 120 1.68 - 1.81: 56 Bond restraints: 7680 Sorted by residual: bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C31 POV D 707 " pdb=" O31 POV D 707 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C31 POV C 703 " pdb=" O31 POV C 703 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C31 POV B 702 " pdb=" O31 POV B 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 7675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 9776 2.38 - 4.77: 349 4.77 - 7.15: 103 7.15 - 9.53: 36 9.53 - 11.92: 16 Bond angle restraints: 10280 Sorted by residual: angle pdb=" O11 POV B 702 " pdb=" P POV B 702 " pdb=" O12 POV B 702 " ideal model delta sigma weight residual 97.67 109.59 -11.92 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV D 704 " pdb=" P POV D 704 " pdb=" O12 POV D 704 " ideal model delta sigma weight residual 97.67 109.58 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV A 701 " pdb=" P POV A 701 " pdb=" O12 POV A 701 " ideal model delta sigma weight residual 97.67 109.56 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV C 703 " pdb=" P POV C 703 " pdb=" O12 POV C 703 " ideal model delta sigma weight residual 97.67 109.56 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV C 703 " pdb=" P POV C 703 " pdb=" O14 POV C 703 " ideal model delta sigma weight residual 121.11 109.40 11.71 3.00e+00 1.11e-01 1.52e+01 ... (remaining 10275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.73: 4172 25.73 - 51.46: 256 51.46 - 77.19: 76 77.19 - 102.91: 0 102.91 - 128.64: 4 Dihedral angle restraints: 4508 sinusoidal: 1916 harmonic: 2592 Sorted by residual: dihedral pdb=" C3 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " pdb=" C32 POV D 704 " ideal model delta sinusoidal sigma weight residual 172.61 43.97 128.64 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C3 POV C 703 " pdb=" C31 POV C 703 " pdb=" O31 POV C 703 " pdb=" C32 POV C 703 " ideal model delta sinusoidal sigma weight residual 172.61 44.00 128.61 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 44.00 128.61 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 4505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 708 0.027 - 0.054: 292 0.054 - 0.081: 148 0.081 - 0.109: 27 0.109 - 0.136: 25 Chirality restraints: 1200 Sorted by residual: chirality pdb=" C2 POV B 702 " pdb=" C1 POV B 702 " pdb=" C3 POV B 702 " pdb=" O21 POV B 702 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C2 POV C 703 " pdb=" C1 POV C 703 " pdb=" C3 POV C 703 " pdb=" O21 POV C 703 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C2 POV A 701 " pdb=" C1 POV A 701 " pdb=" C3 POV A 701 " pdb=" O21 POV A 701 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1197 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 472 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 473 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 472 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 473 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 473 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 473 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO B 473 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.038 5.00e-02 4.00e+02 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 2656 2.88 - 3.44: 8056 3.44 - 4.01: 12339 4.01 - 4.57: 18861 4.57 - 5.14: 26261 Nonbonded interactions: 68173 Sorted by model distance: nonbonded pdb=" O HOH C1002 " pdb=" O HOH C1005 " model vdw 2.313 3.040 nonbonded pdb=" O HOH B1002 " pdb=" O HOH B1005 " model vdw 2.313 3.040 nonbonded pdb=" O HOH A1002 " pdb=" O HOH A1005 " model vdw 2.313 3.040 nonbonded pdb=" O HOH D1002 " pdb=" O HOH D1005 " model vdw 2.313 3.040 nonbonded pdb=" O VAL C 437 " pdb=" OG1 THR C 441 " model vdw 2.353 3.040 ... (remaining 68168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or resid \ 707)) selection = (chain 'B' and (resid 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or resid \ 707)) selection = (chain 'C' and (resid 212 through 701 or (resid 702 and (name C1 or name C2 or n \ ame C3 or name C31 or name C32 or name C33 or name C34 or name C35)) or (resid 7 \ 03 and (name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38)) or (resid 704 through 706 and (name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39)) or (resid 707 and (name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38)))) selection = (chain 'D' and (resid 212 through 489 or (resid 701 through 702 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8)) or (resid 703 and (name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)) or (resid 704 through 706 and (name C32 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or (resi \ d 707 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 \ or name C37 or name C38)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.011 0.116 7680 Z= 0.537 Angle : 1.166 11.916 10280 Z= 0.449 Chirality : 0.039 0.136 1200 Planarity : 0.005 0.068 1192 Dihedral : 17.466 128.642 2812 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 860 helix: 0.81 (0.21), residues: 704 sheet: None (None), residues: 0 loop : 0.20 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 377 TYR 0.003 0.001 TYR A 485 PHE 0.010 0.001 PHE B 290 TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS D 486 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.54 ( 7680) covalent geometry : angle 1.16571 / 0.45 (10280) hydrogen bonds : bond 0.20194 / 13.14 ( 460) hydrogen bonds : angle 4.64250 / 3.32 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.267 Fit side-chains REVERT: A 280 PHE cc_start: 0.7655 (t80) cc_final: 0.7327 (t80) REVERT: A 390 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7506 (ttpt) REVERT: B 280 PHE cc_start: 0.7628 (t80) cc_final: 0.7294 (t80) REVERT: C 280 PHE cc_start: 0.7692 (t80) cc_final: 0.7373 (t80) REVERT: C 390 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7518 (ttpt) REVERT: D 390 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7502 (ttpt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.5023 time to fit residues: 64.8625 Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0040 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 ASN B 313 ASN C 313 ASN D 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127583 restraints weight = 7181.879| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.25 r_work: 0.3324 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7680 Z= 0.127 Angle : 0.516 5.465 10280 Z= 0.264 Chirality : 0.038 0.133 1200 Planarity : 0.005 0.048 1192 Dihedral : 17.138 125.767 1336 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.87 % Allowed : 8.96 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.31), residues: 860 helix: 1.01 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 1.10 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 362 TYR 0.016 0.002 TYR C 483 PHE 0.008 0.001 PHE A 290 TRP 0.003 0.001 TRP D 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 7680) covalent geometry : angle 0.51594 / 0.26 (10280) hydrogen bonds : bond 0.04951 / 3.20 ( 460) hydrogen bonds : angle 3.13273 / 2.17 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.179 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 119 average time/residue: 0.5881 time to fit residues: 72.9371 Evaluate side-chains 102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 486 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 53 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 82 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124207 restraints weight = 7085.126| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.09 r_work: 0.3287 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7680 Z= 0.110 Angle : 0.476 5.417 10280 Z= 0.243 Chirality : 0.038 0.134 1200 Planarity : 0.004 0.047 1192 Dihedral : 14.527 118.890 1336 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.14 % Allowed : 11.23 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.31), residues: 860 helix: 1.24 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 1.15 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.012 0.002 TYR D 485 PHE 0.007 0.001 PHE C 373 TRP 0.005 0.001 TRP D 434 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 7680) covalent geometry : angle 0.47618 / 0.24 (10280) hydrogen bonds : bond 0.03929 / 2.56 ( 460) hydrogen bonds : angle 3.00593 / 2.08 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.160 Fit side-chains REVERT: A 316 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: B 316 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: C 316 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6842 (m-30) outliers start: 16 outliers final: 4 residues processed: 103 average time/residue: 0.6046 time to fit residues: 65.0030 Evaluate side-chains 93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.177435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128387 restraints weight = 7179.047| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.62 r_work: 0.3202 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7680 Z= 0.144 Angle : 0.526 5.384 10280 Z= 0.271 Chirality : 0.040 0.132 1200 Planarity : 0.005 0.052 1192 Dihedral : 13.910 117.509 1336 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.87 % Allowed : 12.30 % Favored : 85.83 % 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 are not related in a simple way. whole: 1.45 (0.30), residues: 860 helix: 1.08 (0.21), residues: 716 sheet: None (None), residues: 0 loop : 0.90 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.017 0.002 TYR A 483 PHE 0.011 0.001 PHE B 373 TRP 0.006 0.001 TRP D 435 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7680) covalent geometry : angle 0.52636 / 0.27 (10280) hydrogen bonds : bond 0.05057 / 3.33 ( 460) hydrogen bonds : angle 3.07409 / 2.13 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.178 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 0.6637 time to fit residues: 66.3353 Evaluate side-chains 91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 418 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134147 restraints weight = 7188.823| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.43 r_work: 0.3219 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.002 0.024 7680 Z= 0.114 Angle : 0.470 5.457 10280 Z= 0.243 Chirality : 0.038 0.126 1200 Planarity : 0.005 0.050 1192 Dihedral : 13.386 114.108 1336 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.14 % Allowed : 12.83 % Favored : 85.03 % 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 are not related in a simple way. whole: 1.73 (0.31), residues: 860 helix: 1.28 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.92 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.019 0.002 TYR D 483 PHE 0.007 0.001 PHE B 404 TRP 0.007 0.001 TRP C 434 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7680) covalent geometry : angle 0.46985 / 0.24 (10280) hydrogen bonds : bond 0.04036 / 2.66 ( 460) hydrogen bonds : angle 2.95634 / 2.04 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.283 Fit side-chains REVERT: B 316 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: C 316 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: D 316 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7041 (m-30) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.6046 time to fit residues: 62.0621 Evaluate side-chains 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.176189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.127045 restraints weight = 7139.728| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7680 Z= 0.142 Angle : 0.518 5.412 10280 Z= 0.268 Chirality : 0.039 0.131 1200 Planarity : 0.005 0.053 1192 Dihedral : 13.677 115.301 1336 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.21 % Allowed : 11.90 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.30), residues: 860 helix: 1.14 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.66 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.016 0.002 TYR D 485 PHE 0.011 0.001 PHE C 404 TRP 0.006 0.001 TRP B 434 HIS 0.002 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7680) covalent geometry : angle 0.51828 / 0.27 (10280) hydrogen bonds : bond 0.05058 / 3.34 ( 460) hydrogen bonds : angle 3.05236 / 2.11 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.156 Fit side-chains REVERT: A 316 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: C 316 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: D 316 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7043 (m-30) outliers start: 24 outliers final: 15 residues processed: 103 average time/residue: 0.5874 time to fit residues: 63.2013 Evaluate side-chains 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0000 chunk 33 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125198 restraints weight = 7102.768| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.23 r_work: 0.3273 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7680 Z= 0.103 Angle : 0.454 5.448 10280 Z= 0.235 Chirality : 0.037 0.119 1200 Planarity : 0.004 0.048 1192 Dihedral : 13.176 111.027 1336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.41 % Allowed : 12.70 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.31), residues: 860 helix: 1.36 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.77 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.019 0.002 TYR A 483 PHE 0.005 0.001 PHE D 404 TRP 0.007 0.001 TRP A 434 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 7680) covalent geometry : angle 0.45403 / 0.23 (10280) hydrogen bonds : bond 0.03479 / 2.29 ( 460) hydrogen bonds : angle 2.87037 / 1.97 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.205 Fit side-chains REVERT: A 316 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: B 316 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: C 316 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: D 316 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7006 (m-30) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 0.6068 time to fit residues: 59.5762 Evaluate side-chains 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.177500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130111 restraints weight = 7149.597| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.14 r_work: 0.3231 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7680 Z= 0.126 Angle : 0.491 5.434 10280 Z= 0.254 Chirality : 0.038 0.128 1200 Planarity : 0.005 0.049 1192 Dihedral : 13.229 112.466 1336 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.81 % Allowed : 12.30 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.31), residues: 860 helix: 1.27 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.72 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.016 0.002 TYR D 485 PHE 0.009 0.001 PHE A 404 TRP 0.005 0.001 TRP C 434 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 7680) covalent geometry : angle 0.49137 / 0.25 (10280) hydrogen bonds : bond 0.04423 / 2.92 ( 460) hydrogen bonds : angle 2.92400 / 2.02 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.250 Fit side-chains REVERT: A 316 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 316 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: C 316 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: D 316 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7027 (m-30) outliers start: 21 outliers final: 16 residues processed: 100 average time/residue: 0.5679 time to fit residues: 59.4339 Evaluate side-chains 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.0030 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127836 restraints weight = 7163.547| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.19 r_work: 0.3287 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7680 Z= 0.102 Angle : 0.455 5.454 10280 Z= 0.234 Chirality : 0.037 0.117 1200 Planarity : 0.004 0.046 1192 Dihedral : 12.728 110.464 1336 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.27 % Allowed : 12.97 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.31), residues: 860 helix: 1.39 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.86 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.021 0.002 TYR B 483 PHE 0.005 0.001 PHE A 404 TRP 0.007 0.001 TRP A 434 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 7680) covalent geometry : angle 0.45459 / 0.23 (10280) hydrogen bonds : bond 0.03408 / 2.24 ( 460) hydrogen bonds : angle 2.82049 / 1.94 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.174 Fit side-chains REVERT: A 316 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: B 316 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: C 316 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: D 316 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.7005 (m-30) outliers start: 17 outliers final: 11 residues processed: 92 average time/residue: 0.5650 time to fit residues: 54.3753 Evaluate side-chains 92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.0040 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121607 restraints weight = 7100.876| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.26 r_work: 0.3239 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7680 Z= 0.108 Angle : 0.468 5.441 10280 Z= 0.241 Chirality : 0.037 0.122 1200 Planarity : 0.004 0.047 1192 Dihedral : 12.569 110.792 1336 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.54 % Allowed : 12.70 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.31), residues: 860 helix: 1.37 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.81 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.022 0.002 TYR C 483 PHE 0.007 0.001 PHE D 404 TRP 0.005 0.001 TRP A 434 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7680) covalent geometry : angle 0.46758 / 0.24 (10280) hydrogen bonds : bond 0.03750 / 2.47 ( 460) hydrogen bonds : angle 2.82863 / 1.95 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.259 Fit side-chains REVERT: A 316 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: B 316 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: C 316 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: D 316 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6948 (m-30) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 0.5909 time to fit residues: 58.9449 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.0030 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122255 restraints weight = 7020.733| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.08 r_work: 0.3253 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7680 Z= 0.118 Angle : 0.482 5.429 10280 Z= 0.249 Chirality : 0.038 0.126 1200 Planarity : 0.005 0.047 1192 Dihedral : 12.507 111.940 1336 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.54 % Allowed : 12.83 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.31), residues: 860 helix: 1.33 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.73 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.022 0.002 TYR B 483 PHE 0.008 0.001 PHE C 404 TRP 0.005 0.001 TRP B 434 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7680) covalent geometry : angle 0.48214 / 0.25 (10280) hydrogen bonds : bond 0.04260 / 2.81 ( 460) hydrogen bonds : angle 2.89031 / 1.99 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.11 seconds wall clock time: 36 minutes 5.40 seconds (2165.40 seconds total)