Starting phenix.real_space_refine on Fri Sep 11 05:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sip_25147/09_2026/7sip_25147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sip_25147/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sip_25147/09_2026/7sip_25147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sip_25147/09_2026/7sip_25147.map" model { file = "/net/cci-nas-00/data/ceres_data/7sip_25147/09_2026/7sip_25147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sip_25147/09_2026/7sip_25147_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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, 169 Unusual residues: {' K': 4, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 1.69, per 1000 atoms: 0.22 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: 0.63 Conformation dependent library (CDL) restraints added in 388.5 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: 0.20 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: 1.00 Time building geometry restraints manager: 0.84 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: 2.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- 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 : 0.265 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: 0.6593 time to fit residues: 85.0614 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 : 0.328 ------------------------------------------------------------------------------- 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: 0.0030 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 = 0.183360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133020 restraints weight = 7156.676| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.93 r_work: 0.3304 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7680 Z= 0.126 Angle : 0.512 5.465 10280 Z= 0.261 Chirality : 0.038 0.128 1200 Planarity : 0.005 0.048 1192 Dihedral : 17.078 125.056 1336 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.87 % Allowed : 8.56 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.30), residues: 860 helix: 1.02 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.42 (0.50), 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 483 PHE 0.008 0.001 PHE A 290 TRP 0.004 0.001 TRP C 434 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 7680) covalent geometry : angle 0.51231 / 0.26 (10280) hydrogen bonds : bond 0.04943 / 3.20 ( 460) hydrogen bonds : angle 3.12547 / 2.16 ( 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 132 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.272 Fit side-chains outliers start: 14 outliers final: 1 residues processed: 120 average time/residue: 0.7230 time to fit residues: 90.6387 Evaluate side-chains 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 2.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.0170 chunk 82 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.182333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125313 restraints weight = 7099.116| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.13 r_work: 0.3280 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7680 Z= 0.110 Angle : 0.472 5.433 10280 Z= 0.242 Chirality : 0.038 0.135 1200 Planarity : 0.004 0.044 1192 Dihedral : 14.757 119.736 1336 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.87 % Allowed : 11.50 % 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: 1.63 (0.30), residues: 860 helix: 1.28 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.52 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.013 0.002 TYR D 485 PHE 0.007 0.001 PHE D 373 TRP 0.006 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 0.47205 / 0.24 (10280) hydrogen bonds : bond 0.03990 / 2.61 ( 460) hydrogen bonds : angle 2.98922 / 2.07 ( 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 109 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.291 Fit side-chains REVERT: C 316 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7003 (m-30) outliers start: 14 outliers final: 4 residues processed: 99 average time/residue: 0.7836 time to fit residues: 80.9863 Evaluate side-chains 93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ILE 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: 0.7980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 0.0030 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 0.0020 chunk 66 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.182667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134885 restraints weight = 7248.827| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.16 r_work: 0.3275 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7680 Z= 0.104 Angle : 0.457 5.421 10280 Z= 0.235 Chirality : 0.037 0.121 1200 Planarity : 0.004 0.045 1192 Dihedral : 13.432 114.199 1336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.20 % Allowed : 13.10 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.76 (0.30), residues: 860 helix: 1.38 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.50 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.018 0.002 TYR B 483 PHE 0.006 0.001 PHE B 404 TRP 0.005 0.001 TRP A 434 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 7680) covalent geometry : angle 0.45727 / 0.23 (10280) hydrogen bonds : bond 0.03540 / 2.32 ( 460) hydrogen bonds : angle 2.86567 / 1.98 ( 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 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.326 Fit side-chains REVERT: A 316 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6884 (m-30) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.8364 time to fit residues: 80.1010 Evaluate side-chains 83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 360 ILE Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 360 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 41 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.180832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127408 restraints weight = 7185.874| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.16 r_work: 0.3266 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2248 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= 0.108 Angle : 0.464 5.405 10280 Z= 0.238 Chirality : 0.038 0.126 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.713 111.518 1336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.27 % Allowed : 12.43 % Favored : 85.29 % 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 are not related in a simple way. whole: 1.79 (0.30), residues: 860 helix: 1.39 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.58 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 362 TYR 0.019 0.002 TYR C 483 PHE 0.007 0.001 PHE B 404 TRP 0.005 0.001 TRP C 434 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 7680) covalent geometry : angle 0.46365 / 0.24 (10280) hydrogen bonds : bond 0.03831 / 2.52 ( 460) hydrogen bonds : angle 2.86443 / 1.98 ( 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 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.274 Fit side-chains REVERT: A 316 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: B 316 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: C 316 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: D 316 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6975 (m-30) outliers start: 17 outliers final: 9 residues processed: 97 average time/residue: 0.7715 time to fit residues: 78.1626 Evaluate side-chains 92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 32 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.4877 > 50:) chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.0030 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 0.0040 chunk 66 optimal weight: 10.0000 overall best weight: 0.5806 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.180166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125482 restraints weight = 7182.759| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.30 r_work: 0.3261 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7680 Z= 0.109 Angle : 0.463 5.394 10280 Z= 0.238 Chirality : 0.038 0.125 1200 Planarity : 0.004 0.049 1192 Dihedral : 12.605 111.431 1336 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.67 % Allowed : 12.30 % 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: 1.77 (0.30), residues: 860 helix: 1.38 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.48 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.013 0.001 TYR D 485 PHE 0.007 0.001 PHE A 404 TRP 0.006 0.001 TRP B 434 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7680) covalent geometry : angle 0.46273 / 0.24 (10280) hydrogen bonds : bond 0.03849 / 2.54 ( 460) hydrogen bonds : angle 2.85356 / 1.97 ( 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 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.269 Fit side-chains REVERT: A 316 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6958 (m-30) REVERT: B 316 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: C 316 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: D 316 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7012 (m-30) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.7163 time to fit residues: 71.9333 Evaluate side-chains 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 54 optimal weight: 0.5980 overall best weight: 0.1424 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.184697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127844 restraints weight = 7130.149| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.19 r_work: 0.3309 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7680 Z= 0.095 Angle : 0.438 5.437 10280 Z= 0.223 Chirality : 0.036 0.114 1200 Planarity : 0.004 0.044 1192 Dihedral : 11.883 108.807 1336 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: 1.90 (0.31), residues: 860 helix: 1.48 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.52 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.021 0.002 TYR B 483 PHE 0.004 0.000 PHE D 433 TRP 0.007 0.001 TRP A 434 HIS 0.000 0.000 HIS B 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.10 ( 7680) covalent geometry : angle 0.43762 / 0.22 (10280) hydrogen bonds : bond 0.02858 / 1.87 ( 460) hydrogen bonds : angle 2.71249 / 1.86 ( 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 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.262 Fit side-chains REVERT: A 316 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: B 316 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: C 316 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: D 316 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6887 (m-30) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.7259 time to fit residues: 74.4041 Evaluate side-chains 97 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 321 ILE 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: 0.6980 chunk 81 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.176718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120166 restraints weight = 7080.257| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.20 r_work: 0.3210 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7680 Z= 0.143 Angle : 0.517 5.382 10280 Z= 0.267 Chirality : 0.039 0.145 1200 Planarity : 0.005 0.050 1192 Dihedral : 12.896 113.266 1336 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.87 % Allowed : 13.64 % Favored : 84.49 % 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: 1.63 (0.30), residues: 860 helix: 1.30 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.33 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.018 0.002 TYR D 485 PHE 0.011 0.001 PHE D 404 TRP 0.007 0.001 TRP B 435 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7680) covalent geometry : angle 0.51742 / 0.27 (10280) hydrogen bonds : bond 0.04924 / 3.26 ( 460) hydrogen bonds : angle 2.96970 / 2.06 ( 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 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.279 Fit side-chains REVERT: A 316 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: B 316 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: C 316 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: D 316 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7193 (m-30) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.7562 time to fit residues: 77.4369 Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 63 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.179986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122769 restraints weight = 7122.800| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.17 r_work: 0.3241 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7680 Z= 0.106 Angle : 0.457 5.425 10280 Z= 0.236 Chirality : 0.037 0.122 1200 Planarity : 0.004 0.051 1192 Dihedral : 12.535 111.545 1336 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.27 % Allowed : 13.37 % Favored : 84.36 % 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 (0.30), residues: 860 helix: 1.43 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.43 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.020 0.002 TYR A 483 PHE 0.006 0.001 PHE D 404 TRP 0.007 0.001 TRP C 434 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 7680) covalent geometry : angle 0.45684 / 0.24 (10280) hydrogen bonds : bond 0.03755 / 2.47 ( 460) hydrogen bonds : angle 2.84140 / 1.96 ( 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 98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.274 Fit side-chains REVERT: A 316 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: B 316 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: C 316 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: D 316 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7020 (m-30) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.7422 time to fit residues: 74.5807 Evaluate side-chains 95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.178781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122566 restraints weight = 7034.148| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.17 r_work: 0.3226 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7680 Z= 0.116 Angle : 0.475 5.406 10280 Z= 0.246 Chirality : 0.038 0.129 1200 Planarity : 0.004 0.051 1192 Dihedral : 12.775 112.043 1336 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.01 % Allowed : 13.77 % Favored : 84.22 % 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 (0.30), residues: 860 helix: 1.37 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.38 (0.50), 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 0.008 0.001 PHE B 404 TRP 0.005 0.001 TRP B 434 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7680) covalent geometry : angle 0.47509 / 0.25 (10280) hydrogen bonds : bond 0.04133 / 2.73 ( 460) hydrogen bonds : angle 2.86589 / 1.98 ( 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 96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.291 Fit side-chains REVERT: A 316 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: B 316 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: C 316 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: D 316 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7043 (m-30) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.7331 time to fit residues: 72.9026 Evaluate side-chains 94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.179462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123182 restraints weight = 7031.648| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.30 r_work: 0.3250 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2682 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= 0.107 Angle : 0.459 5.422 10280 Z= 0.237 Chirality : 0.037 0.122 1200 Planarity : 0.005 0.050 1192 Dihedral : 12.559 111.464 1336 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.01 % Allowed : 13.77 % Favored : 84.22 % 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: 1.81 (0.30), residues: 860 helix: 1.42 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.46 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.022 0.003 TYR A 483 PHE 0.006 0.001 PHE B 404 TRP 0.006 0.001 TRP A 434 HIS 0.001 0.000 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 7680) covalent geometry : angle 0.45857 / 0.24 (10280) hydrogen bonds : bond 0.03794 / 2.50 ( 460) hydrogen bonds : angle 2.81877 / 1.95 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.66 seconds wall clock time: 44 minutes 0.38 seconds (2640.38 seconds total)