Starting phenix.real_space_refine on Wed Feb 12 11:45:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sip_25147/02_2025/7sip_25147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sip_25147/02_2025/7sip_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_25147/02_2025/7sip_25147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sip_25147/02_2025/7sip_25147.map" model { file = "/net/cci-nas-00/data/ceres_data/7sip_25147/02_2025/7sip_25147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sip_25147/02_2025/7sip_25147_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'GLU:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 4, '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: {'TYR:plan': 1, 'GLU:plan': 4, '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-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} 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-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} 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-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} 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-3': 3, 'POV:plan-2': 6, 'POV:plan-1': 6} 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: 5.29, per 1000 atoms: 0.70 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: 1.98 Conformation dependent library (CDL) restraints added in 873.1 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: 0.73 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: 1.87 Time building geometry restraints manager: 2.28 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 489 or resid 701 or (resid 702 and (name C1 or \ name C2 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35) \ ) 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 n \ ame C34 or name 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: 1.740 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.100 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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= 0.690 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (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 TRP 0.008 0.001 TRP C 434 HIS 0.001 0.000 HIS D 486 PHE 0.010 0.001 PHE B 290 TYR 0.003 0.001 TYR A 485 ARG 0.007 0.001 ARG B 377 *********************** 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 : 0.752 Fit side-chains REVERT: A 280 PHE cc_start: 0.7654 (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: 0.7293 (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: 1.4376 time to fit residues: 185.2870 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 : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.180336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123368 restraints weight = 7088.418| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.86 r_work: 0.3253 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1467 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= 0.192 Angle : 0.535 5.461 10280 Z= 0.275 Chirality : 0.039 0.137 1200 Planarity : 0.005 0.051 1192 Dihedral : 17.187 127.321 1336 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.01 % Allowed : 8.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.30), residues: 860 helix: 0.93 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.40 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 434 HIS 0.001 0.000 HIS B 378 PHE 0.009 0.001 PHE B 373 TYR 0.016 0.002 TYR C 483 ARG 0.004 0.000 ARG A 362 *********************** 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: 15 poor density : 117 time to evaluate : 0.884 Fit side-chains outliers start: 15 outliers final: 3 residues processed: 119 average time/residue: 1.6518 time to fit residues: 205.0639 Evaluate side-chains 103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain D residue 295 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.0040 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.4450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.181369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127429 restraints weight = 7135.729| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.23 r_work: 0.3276 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1880 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= 0.141 Angle : 0.468 5.440 10280 Z= 0.242 Chirality : 0.038 0.124 1200 Planarity : 0.004 0.047 1192 Dihedral : 14.859 121.254 1336 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.87 % Allowed : 11.76 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.30), residues: 860 helix: 1.25 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.56 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 434 HIS 0.001 0.000 HIS D 378 PHE 0.006 0.001 PHE B 290 TYR 0.011 0.002 TYR D 485 ARG 0.004 0.000 ARG A 362 *********************** 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 112 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.854 Fit side-chains REVERT: C 316 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7022 (m-30) outliers start: 14 outliers final: 5 residues processed: 102 average time/residue: 1.6835 time to fit residues: 179.1677 Evaluate side-chains 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 486 HIS Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 486 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123799 restraints weight = 7150.471| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.16 r_work: 0.3257 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2116 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= 0.143 Angle : 0.466 5.415 10280 Z= 0.240 Chirality : 0.038 0.124 1200 Planarity : 0.004 0.048 1192 Dihedral : 13.359 115.166 1336 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.60 % Allowed : 12.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.30), residues: 860 helix: 1.34 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.48 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 434 HIS 0.001 0.000 HIS B 378 PHE 0.007 0.001 PHE C 404 TYR 0.020 0.002 TYR C 483 ARG 0.004 0.000 ARG C 362 *********************** 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 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.761 Fit side-chains REVERT: A 316 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6902 (m-30) outliers start: 12 outliers final: 4 residues processed: 93 average time/residue: 1.6874 time to fit residues: 163.7440 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 : 0.815 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121380 restraints weight = 7023.955| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.16 r_work: 0.3209 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7680 Z= 0.192 Angle : 0.502 5.372 10280 Z= 0.259 Chirality : 0.039 0.138 1200 Planarity : 0.005 0.051 1192 Dihedral : 13.363 114.840 1336 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.81 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.30), residues: 860 helix: 1.19 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.38 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 434 HIS 0.001 0.001 HIS B 378 PHE 0.009 0.001 PHE D 404 TYR 0.016 0.002 TYR B 485 ARG 0.003 0.000 ARG C 362 *********************** 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 109 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.771 Fit side-chains REVERT: A 316 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: B 316 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: C 316 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6965 (m-30) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 1.5830 time to fit residues: 179.0521 Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 311 VAL 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 418 GLU 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 B residue 418 GLU Chi-restraints excluded: chain C residue 295 THR 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 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 83 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123371 restraints weight = 7133.205| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.31 r_work: 0.3254 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7680 Z= 0.161 Angle : 0.470 5.400 10280 Z= 0.244 Chirality : 0.038 0.126 1200 Planarity : 0.005 0.050 1192 Dihedral : 12.981 113.059 1336 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.14 % Allowed : 13.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.30), residues: 860 helix: 1.28 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 434 HIS 0.001 0.000 HIS D 378 PHE 0.007 0.001 PHE D 404 TYR 0.020 0.002 TYR C 483 ARG 0.003 0.000 ARG C 362 *********************** 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 99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.777 Fit side-chains REVERT: A 316 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: B 316 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7214 (m-30) REVERT: C 316 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7114 (m-30) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 1.5848 time to fit residues: 160.6372 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 : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL 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 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 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.178555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122572 restraints weight = 7036.678| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.20 r_work: 0.3241 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2588 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= 0.162 Angle : 0.472 5.408 10280 Z= 0.244 Chirality : 0.038 0.128 1200 Planarity : 0.004 0.048 1192 Dihedral : 12.701 112.052 1336 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.81 % Allowed : 12.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.30), residues: 860 helix: 1.32 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.33 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 434 HIS 0.001 0.001 HIS D 378 PHE 0.008 0.001 PHE A 404 TYR 0.015 0.002 TYR B 485 ARG 0.002 0.000 ARG B 297 *********************** 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 101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.765 Fit side-chains REVERT: A 316 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: B 316 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: C 316 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: D 316 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7066 (m-30) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 1.5231 time to fit residues: 152.9205 Evaluate side-chains 100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL 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 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 295 THR 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 62 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120194 restraints weight = 7085.192| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.28 r_work: 0.3215 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2638 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= 0.187 Angle : 0.489 5.404 10280 Z= 0.253 Chirality : 0.038 0.130 1200 Planarity : 0.005 0.049 1192 Dihedral : 12.732 113.174 1336 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.21 % Allowed : 12.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.30), residues: 860 helix: 1.26 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.26 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 434 HIS 0.001 0.001 HIS D 378 PHE 0.009 0.001 PHE C 404 TYR 0.022 0.003 TYR C 483 ARG 0.002 0.000 ARG C 297 *********************** 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 111 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.812 Fit side-chains REVERT: A 316 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: B 316 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: C 316 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7026 (m-30) REVERT: D 316 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7077 (m-30) outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 1.5912 time to fit residues: 173.0516 Evaluate side-chains 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL 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 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 B residue 418 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 295 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.176378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120843 restraints weight = 7144.400| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.21 r_work: 0.3210 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2741 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= 0.194 Angle : 0.492 5.405 10280 Z= 0.256 Chirality : 0.039 0.132 1200 Planarity : 0.005 0.048 1192 Dihedral : 12.549 113.402 1336 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.94 % Allowed : 12.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.30), residues: 860 helix: 1.22 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.32 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 434 HIS 0.001 0.001 HIS D 378 PHE 0.009 0.001 PHE C 404 TYR 0.016 0.002 TYR D 485 ARG 0.002 0.000 ARG C 362 *********************** 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 106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.817 Fit side-chains REVERT: A 316 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: B 316 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7040 (m-30) REVERT: C 316 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7050 (m-30) REVERT: D 316 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7066 (m-30) outliers start: 22 outliers final: 15 residues processed: 102 average time/residue: 1.6700 time to fit residues: 177.7580 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 : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 311 VAL 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 295 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 316 ASP 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 295 THR 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 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.177798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122366 restraints weight = 7091.928| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.19 r_work: 0.3232 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2743 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= 0.167 Angle : 0.473 5.424 10280 Z= 0.245 Chirality : 0.038 0.124 1200 Planarity : 0.005 0.048 1192 Dihedral : 12.208 112.091 1336 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.81 % Allowed : 12.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 860 helix: 1.29 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.37 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 434 HIS 0.001 0.000 HIS B 378 PHE 0.007 0.001 PHE C 404 TYR 0.021 0.003 TYR A 483 ARG 0.002 0.000 ARG B 297 ********************** 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 105 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.807 Fit side-chains REVERT: A 316 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: B 316 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: C 316 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: D 316 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7059 (m-30) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 1.5468 time to fit residues: 165.0320 Evaluate side-chains 104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL 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 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 B residue 418 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 295 THR 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 79 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.177393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122158 restraints weight = 7024.513| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.15 r_work: 0.3217 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2819 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= 0.171 Angle : 0.479 5.426 10280 Z= 0.249 Chirality : 0.038 0.126 1200 Planarity : 0.005 0.047 1192 Dihedral : 12.155 112.066 1336 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.07 % Allowed : 12.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 860 helix: 1.28 (0.21), residues: 712 sheet: None (None), residues: 0 loop : 0.43 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 434 HIS 0.001 0.000 HIS B 378 PHE 0.008 0.001 PHE B 404 TYR 0.016 0.002 TYR D 485 ARG 0.002 0.000 ARG C 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.90 seconds wall clock time: 91 minutes 27.94 seconds (5487.94 seconds total)