Starting phenix.real_space_refine on Wed Mar 4 23:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.map" model { file = "/net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u9e_20695/03_2026/6u9e_20695.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 10881 2.51 5 N 2871 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 3.92, per 1000 atoms: 0.23 Number of scatterers: 17175 At special positions: 0 Unit cell: (103.79, 103.79, 206.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3387 8.00 N 2871 7.00 C 10881 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: 1.45 Conformation dependent library (CDL) restraints added in 805.2 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 40 sheets defined 8.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.909A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.671A pdb=" N LYS A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.625A pdb=" N GLN A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.575A pdb=" N GLN A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.869A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 578 " --> pdb=" O CYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 701 " --> pdb=" O LYS A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 701' Processing helix chain 'A' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.908A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 328 through 335 Processing helix chain 'C' and resid 347 through 353 removed outlier: 3.670A pdb=" N LYS C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.624A pdb=" N GLN C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.574A pdb=" N GLN C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.870A pdb=" N LYS C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 578 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET C 700 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 701 " --> pdb=" O LYS C 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 697 through 701' Processing helix chain 'C' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN C 776 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 removed outlier: 3.908A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 254' Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 347 through 353 removed outlier: 3.671A pdb=" N LYS E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 398 removed outlier: 3.624A pdb=" N GLN E 395 " --> pdb=" O PHE E 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 396 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.575A pdb=" N GLN E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 removed outlier: 3.869A pdb=" N LYS E 576 " --> pdb=" O LYS E 572 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 578 " --> pdb=" O CYS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET E 700 " --> pdb=" O ALA E 697 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 701 " --> pdb=" O LYS E 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 697 through 701' Processing helix chain 'E' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN E 776 " --> pdb=" O SER E 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER A 269 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 187 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.638A pdb=" N CYS A 227 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 223 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 239 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 301 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.638A pdb=" N CYS A 227 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 564 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS A 616 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG A 564 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 614 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 451 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR A 416 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA7, first strand: chain 'A' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS A 466 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 640 removed outlier: 6.857A pdb=" N LEU A 736 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 692 through 695 removed outlier: 3.603A pdb=" N LEU A 713 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB2, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.540A pdb=" N SER A 802 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 814 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER C 269 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 187 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 300 through 301 removed outlier: 3.520A pdb=" N HIS C 301 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 239 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 227 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS C 223 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 564 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS C 616 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG C 564 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 614 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 451 " --> pdb=" O THR C 526 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR C 416 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 461 through 462 Processing sheet with id=AB8, first strand: chain 'C' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS C 466 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 640 removed outlier: 6.856A pdb=" N LEU C 736 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 692 through 695 removed outlier: 3.603A pdb=" N LEU C 713 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 781 through 783 Processing sheet with id=AC3, first strand: chain 'C' and resid 800 through 802 removed outlier: 3.540A pdb=" N SER C 802 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 814 " --> pdb=" O SER C 802 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER E 269 " --> pdb=" O LYS E 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS E 187 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 301 removed outlier: 3.520A pdb=" N HIS E 301 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 239 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 227 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 223 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 564 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS E 616 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG E 564 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 614 " --> pdb=" O ARG E 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 451 " --> pdb=" O THR E 526 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 342 through 344 Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR E 416 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 461 through 462 Processing sheet with id=AC9, first strand: chain 'E' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS E 466 " --> pdb=" O ASN E 499 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 637 through 640 removed outlier: 6.857A pdb=" N LEU E 736 " --> pdb=" O ILE E 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 692 through 695 removed outlier: 3.602A pdb=" N LEU E 713 " --> pdb=" O TYR E 692 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 781 through 783 Processing sheet with id=AD4, first strand: chain 'E' and resid 800 through 802 removed outlier: 3.539A pdb=" N SER E 802 " --> pdb=" O ARG E 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG E 814 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.589A pdb=" N LEU B 15 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.536A pdb=" N ILE B 44 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN F 55 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER B 46 " --> pdb=" O ASN F 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.537A pdb=" N ASN B 55 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.514A pdb=" N SER B 76 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 100 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN D 116 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 124 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 123 " --> pdb=" O ILE F 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.657A pdb=" N ILE D 125 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP D 124 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 107 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.509A pdb=" N ILE D 132 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE F 125 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 117 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN B 116 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 76 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.588A pdb=" N LEU D 15 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.176A pdb=" N GLN D 51 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER F 46 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 53 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.588A pdb=" N LEU F 15 " --> pdb=" O LEU F 30 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 891 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: 3.01 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5385 1.33 - 1.45: 2417 1.45 - 1.57: 9583 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 17430 Sorted by residual: bond pdb=" CA ASN C 723 " pdb=" C ASN C 723 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.80e-02 3.09e+03 5.07e+00 bond pdb=" CA ASN E 723 " pdb=" C ASN E 723 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.80e-02 3.09e+03 5.07e+00 bond pdb=" CA ASN A 723 " pdb=" C ASN A 723 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.80e-02 3.09e+03 5.04e+00 bond pdb=" CB ASN A 387 " pdb=" CG ASN A 387 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.35e+00 bond pdb=" CB ASN E 387 " pdb=" CG ASN E 387 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.32e+00 ... (remaining 17425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 21982 2.01 - 4.02: 1262 4.02 - 6.03: 174 6.03 - 8.04: 39 8.04 - 10.05: 18 Bond angle restraints: 23475 Sorted by residual: angle pdb=" N SER D 127 " pdb=" CA SER D 127 " pdb=" C SER D 127 " ideal model delta sigma weight residual 107.73 114.15 -6.42 1.34e+00 5.57e-01 2.30e+01 angle pdb=" N SER B 127 " pdb=" CA SER B 127 " pdb=" C SER B 127 " ideal model delta sigma weight residual 107.73 114.15 -6.42 1.34e+00 5.57e-01 2.29e+01 angle pdb=" N SER F 127 " pdb=" CA SER F 127 " pdb=" C SER F 127 " ideal model delta sigma weight residual 107.73 114.12 -6.39 1.34e+00 5.57e-01 2.27e+01 angle pdb=" N SER E 558 " pdb=" CA SER E 558 " pdb=" C SER E 558 " ideal model delta sigma weight residual 110.24 116.06 -5.82 1.30e+00 5.92e-01 2.00e+01 angle pdb=" N SER A 558 " pdb=" CA SER A 558 " pdb=" C SER A 558 " ideal model delta sigma weight residual 110.24 116.05 -5.81 1.30e+00 5.92e-01 2.00e+01 ... (remaining 23470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 10194 14.80 - 29.61: 533 29.61 - 44.41: 54 44.41 - 59.22: 1 59.22 - 74.02: 3 Dihedral angle restraints: 10785 sinusoidal: 4404 harmonic: 6381 Sorted by residual: dihedral pdb=" CA ASN C 218 " pdb=" C ASN C 218 " pdb=" N PRO C 219 " pdb=" CA PRO C 219 " ideal model delta harmonic sigma weight residual -180.00 -141.75 -38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA ASN E 218 " pdb=" C ASN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N PRO A 219 " pdb=" CA PRO A 219 " ideal model delta harmonic sigma weight residual -180.00 -141.81 -38.19 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 10782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1618 0.051 - 0.101: 738 0.101 - 0.152: 288 0.152 - 0.203: 42 0.203 - 0.254: 11 Chirality restraints: 2697 Sorted by residual: chirality pdb=" CB ILE A 455 " pdb=" CA ILE A 455 " pdb=" CG1 ILE A 455 " pdb=" CG2 ILE A 455 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 455 " pdb=" CA ILE C 455 " pdb=" CG1 ILE C 455 " pdb=" CG2 ILE C 455 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE E 455 " pdb=" CA ILE E 455 " pdb=" CG1 ILE E 455 " pdb=" CG2 ILE E 455 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2694 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 673 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C GLN A 673 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 673 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 674 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 673 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C GLN E 673 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN E 673 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU E 674 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 673 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C GLN C 673 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN C 673 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU C 674 " 0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3013 2.76 - 3.30: 14065 3.30 - 3.83: 25765 3.83 - 4.37: 29322 4.37 - 4.90: 52128 Nonbonded interactions: 124293 Sorted by model distance: nonbonded pdb=" O TYR C 505 " pdb=" OG SER C 686 " model vdw 2.228 3.040 nonbonded pdb=" O TYR A 505 " pdb=" OG SER A 686 " model vdw 2.229 3.040 nonbonded pdb=" O TYR E 505 " pdb=" OG SER E 686 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 773 " pdb=" OE1 GLN E 783 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 72 " pdb=" OG SER B 75 " model vdw 2.283 3.040 ... (remaining 124288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.008 0.076 17430 Z= 0.378 Angle : 1.081 10.046 23475 Z= 0.597 Chirality : 0.064 0.254 2697 Planarity : 0.005 0.048 3012 Dihedral : 9.089 74.022 6603 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 5.88 % Twisted General : 0.72 % 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: -4.33 (0.15), residues: 2112 helix: -4.47 (0.17), residues: 150 sheet: -1.84 (0.19), residues: 705 loop : -3.45 (0.14), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 478 TYR 0.029 0.003 TYR A 712 PHE 0.024 0.004 PHE E 293 TRP 0.014 0.002 TRP A 334 HIS 0.013 0.003 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00847 (17430) covalent geometry : angle 1.08099 (23475) hydrogen bonds : bond 0.29660 ( 333) hydrogen bonds : angle 10.97980 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8844 (m-30) cc_final: 0.8486 (m-30) REVERT: A 488 LEU cc_start: 0.7856 (mt) cc_final: 0.7513 (pp) REVERT: A 506 ILE cc_start: 0.8994 (mt) cc_final: 0.8687 (tt) REVERT: A 639 ASN cc_start: 0.8231 (t0) cc_final: 0.7769 (p0) REVERT: A 689 ASP cc_start: 0.7944 (m-30) cc_final: 0.7646 (t0) REVERT: A 733 ASP cc_start: 0.8323 (m-30) cc_final: 0.7995 (m-30) REVERT: C 225 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 326 PHE cc_start: 0.8423 (m-80) cc_final: 0.7579 (m-10) REVERT: C 390 ASP cc_start: 0.8998 (m-30) cc_final: 0.8668 (m-30) REVERT: C 488 LEU cc_start: 0.8496 (mt) cc_final: 0.8224 (pp) REVERT: C 506 ILE cc_start: 0.9016 (mt) cc_final: 0.8715 (tt) REVERT: C 689 ASP cc_start: 0.7913 (m-30) cc_final: 0.7485 (t70) REVERT: C 792 LEU cc_start: 0.9125 (mt) cc_final: 0.8739 (tt) REVERT: E 390 ASP cc_start: 0.8786 (m-30) cc_final: 0.8324 (m-30) REVERT: E 488 LEU cc_start: 0.8892 (mt) cc_final: 0.8565 (pp) REVERT: E 506 ILE cc_start: 0.8963 (mt) cc_final: 0.8566 (tt) REVERT: E 527 SER cc_start: 0.9140 (m) cc_final: 0.8665 (p) REVERT: E 536 THR cc_start: 0.8085 (p) cc_final: 0.7855 (p) REVERT: E 544 ASP cc_start: 0.7608 (m-30) cc_final: 0.7408 (t70) REVERT: E 545 ASN cc_start: 0.7035 (m-40) cc_final: 0.6404 (t0) REVERT: E 751 ILE cc_start: 0.8664 (mt) cc_final: 0.8249 (mm) REVERT: E 792 LEU cc_start: 0.9147 (mt) cc_final: 0.8732 (tt) REVERT: B 52 ILE cc_start: 0.9485 (mt) cc_final: 0.9024 (mm) REVERT: F 26 CYS cc_start: 0.8428 (m) cc_final: 0.8037 (p) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1270 time to fit residues: 88.1102 Evaluate side-chains 224 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 395 GLN A 452 GLN A 499 ASN C 192 ASN C 753 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN E 545 ASN E 548 ASN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 118 GLN D 118 GLN F 90 ASN F 118 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084048 restraints weight = 29617.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084742 restraints weight = 25844.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085423 restraints weight = 18026.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086448 restraints weight = 15780.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087140 restraints weight = 13652.119| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17430 Z= 0.148 Angle : 0.672 7.464 23475 Z= 0.361 Chirality : 0.051 0.193 2697 Planarity : 0.003 0.052 3012 Dihedral : 7.184 30.496 2241 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.10 % Allowed : 2.24 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.94 (0.16), residues: 2112 helix: -3.35 (0.26), residues: 162 sheet: -1.65 (0.19), residues: 678 loop : -3.22 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.014 0.001 TYR E 341 PHE 0.014 0.001 PHE A 362 TRP 0.019 0.002 TRP A 236 HIS 0.005 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00331 (17430) covalent geometry : angle 0.67171 (23475) hydrogen bonds : bond 0.03034 ( 333) hydrogen bonds : angle 6.55420 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 327 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7037 (tt0) REVERT: A 390 ASP cc_start: 0.9269 (m-30) cc_final: 0.8978 (m-30) REVERT: A 527 SER cc_start: 0.8778 (m) cc_final: 0.8564 (t) REVERT: A 685 ASN cc_start: 0.6198 (t0) cc_final: 0.5978 (t0) REVERT: A 689 ASP cc_start: 0.8248 (m-30) cc_final: 0.7998 (t0) REVERT: C 326 PHE cc_start: 0.8225 (m-80) cc_final: 0.7744 (m-10) REVERT: C 506 ILE cc_start: 0.9047 (mt) cc_final: 0.8799 (tt) REVERT: C 535 ASP cc_start: 0.8060 (m-30) cc_final: 0.7708 (m-30) REVERT: C 689 ASP cc_start: 0.8156 (m-30) cc_final: 0.7683 (t0) REVERT: C 778 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7875 (mp0) REVERT: C 792 LEU cc_start: 0.8849 (mt) cc_final: 0.8394 (tt) REVERT: E 192 ASN cc_start: 0.8638 (m-40) cc_final: 0.8390 (t0) REVERT: E 328 ASP cc_start: 0.8385 (p0) cc_final: 0.8182 (p0) REVERT: E 330 LEU cc_start: 0.9216 (tp) cc_final: 0.8949 (tp) REVERT: E 454 LEU cc_start: 0.9098 (tp) cc_final: 0.8818 (tp) REVERT: E 506 ILE cc_start: 0.8940 (mt) cc_final: 0.8622 (tt) REVERT: E 527 SER cc_start: 0.9116 (m) cc_final: 0.8439 (p) REVERT: E 544 ASP cc_start: 0.7694 (m-30) cc_final: 0.7225 (t70) REVERT: E 545 ASN cc_start: 0.6978 (m110) cc_final: 0.6673 (t0) REVERT: B 83 LYS cc_start: 0.7731 (mttt) cc_final: 0.7414 (tttt) REVERT: D 52 ILE cc_start: 0.9266 (mt) cc_final: 0.8920 (mm) REVERT: F 104 SER cc_start: 0.7857 (p) cc_final: 0.7514 (p) outliers start: 2 outliers final: 0 residues processed: 329 average time/residue: 0.1069 time to fit residues: 56.3334 Evaluate side-chains 186 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 62 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN C 265 GLN C 499 ASN E 211 HIS E 378 GLN E 452 GLN E 529 ASN E 548 ASN D 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.101119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083039 restraints weight = 30696.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083642 restraints weight = 26102.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084236 restraints weight = 19328.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084807 restraints weight = 16917.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085161 restraints weight = 15126.942| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17430 Z= 0.146 Angle : 0.638 8.666 23475 Z= 0.341 Chirality : 0.050 0.201 2697 Planarity : 0.003 0.057 3012 Dihedral : 6.643 30.100 2241 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.15 % Allowed : 1.93 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.61 (0.16), residues: 2112 helix: -2.78 (0.31), residues: 162 sheet: -1.38 (0.20), residues: 666 loop : -3.07 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 564 TYR 0.011 0.001 TYR E 712 PHE 0.009 0.001 PHE C 352 TRP 0.021 0.002 TRP A 236 HIS 0.004 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00328 (17430) covalent geometry : angle 0.63836 (23475) hydrogen bonds : bond 0.02976 ( 333) hydrogen bonds : angle 5.73717 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9179 (m-30) cc_final: 0.8932 (m-30) REVERT: A 440 LYS cc_start: 0.7283 (mptt) cc_final: 0.6677 (tptp) REVERT: A 689 ASP cc_start: 0.8270 (m-30) cc_final: 0.7968 (t0) REVERT: A 700 MET cc_start: 0.8342 (mtm) cc_final: 0.8051 (mtp) REVERT: C 254 LEU cc_start: 0.8308 (mt) cc_final: 0.8071 (mt) REVERT: C 506 ILE cc_start: 0.9109 (mt) cc_final: 0.8881 (tt) REVERT: C 689 ASP cc_start: 0.8252 (m-30) cc_final: 0.7983 (t0) REVERT: C 778 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7822 (mp0) REVERT: C 792 LEU cc_start: 0.8973 (mt) cc_final: 0.8548 (tt) REVERT: E 226 VAL cc_start: 0.9470 (t) cc_final: 0.9124 (p) REVERT: E 252 PHE cc_start: 0.7989 (m-80) cc_final: 0.7644 (m-10) REVERT: E 263 ASP cc_start: 0.7706 (t70) cc_final: 0.7230 (t70) REVERT: E 330 LEU cc_start: 0.9313 (tp) cc_final: 0.9046 (tp) REVERT: E 454 LEU cc_start: 0.9235 (tp) cc_final: 0.8949 (tp) REVERT: E 506 ILE cc_start: 0.8801 (mt) cc_final: 0.8448 (tt) REVERT: E 527 SER cc_start: 0.9177 (m) cc_final: 0.8572 (p) REVERT: E 544 ASP cc_start: 0.7732 (m-30) cc_final: 0.7347 (t70) REVERT: E 545 ASN cc_start: 0.6946 (m110) cc_final: 0.6530 (t0) REVERT: E 563 GLN cc_start: 0.8397 (mt0) cc_final: 0.8174 (mt0) REVERT: E 710 ILE cc_start: 0.9565 (mt) cc_final: 0.9309 (tp) REVERT: B 9 ASN cc_start: 0.9223 (m-40) cc_final: 0.8774 (t0) REVERT: B 42 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 83 LYS cc_start: 0.7767 (mttt) cc_final: 0.7327 (tttt) REVERT: D 52 ILE cc_start: 0.9354 (mt) cc_final: 0.8967 (mm) REVERT: F 54 GLU cc_start: 0.7870 (mp0) cc_final: 0.7604 (mp0) outliers start: 3 outliers final: 2 residues processed: 265 average time/residue: 0.1023 time to fit residues: 44.0308 Evaluate side-chains 167 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 189 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 563 GLN E 192 ASN E 370 ASN E 753 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080452 restraints weight = 31214.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081567 restraints weight = 26620.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082240 restraints weight = 17392.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.083948 restraints weight = 15369.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084029 restraints weight = 11542.487| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17430 Z= 0.163 Angle : 0.639 7.287 23475 Z= 0.342 Chirality : 0.050 0.225 2697 Planarity : 0.003 0.058 3012 Dihedral : 6.479 28.263 2241 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.43 (0.17), residues: 2112 helix: -2.41 (0.34), residues: 162 sheet: -1.28 (0.20), residues: 696 loop : -2.99 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.014 0.001 TYR A 692 PHE 0.011 0.001 PHE E 326 TRP 0.017 0.002 TRP A 236 HIS 0.004 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00373 (17430) covalent geometry : angle 0.63935 (23475) hydrogen bonds : bond 0.02837 ( 333) hydrogen bonds : angle 5.43000 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9195 (m-30) cc_final: 0.8960 (m-30) REVERT: A 440 LYS cc_start: 0.7423 (mptt) cc_final: 0.6698 (tptp) REVERT: A 563 GLN cc_start: 0.8579 (mt0) cc_final: 0.8231 (pt0) REVERT: A 700 MET cc_start: 0.8441 (mtm) cc_final: 0.8213 (mtp) REVERT: C 254 LEU cc_start: 0.8377 (mt) cc_final: 0.8157 (mt) REVERT: C 778 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7751 (mp0) REVERT: E 225 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7964 (mt-10) REVERT: E 226 VAL cc_start: 0.9530 (t) cc_final: 0.9275 (p) REVERT: E 263 ASP cc_start: 0.7707 (t70) cc_final: 0.7249 (t70) REVERT: E 330 LEU cc_start: 0.9289 (tp) cc_final: 0.9080 (tp) REVERT: E 390 ASP cc_start: 0.9222 (m-30) cc_final: 0.8933 (m-30) REVERT: E 454 LEU cc_start: 0.9198 (tp) cc_final: 0.8948 (tp) REVERT: E 506 ILE cc_start: 0.8748 (mt) cc_final: 0.8402 (tt) REVERT: E 522 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6842 (mm-30) REVERT: E 544 ASP cc_start: 0.7788 (m-30) cc_final: 0.7252 (t70) REVERT: E 545 ASN cc_start: 0.6979 (m110) cc_final: 0.6695 (t0) REVERT: B 9 ASN cc_start: 0.9172 (m-40) cc_final: 0.8845 (t0) REVERT: B 83 LYS cc_start: 0.7780 (mttt) cc_final: 0.7425 (tttt) REVERT: D 29 LYS cc_start: 0.8841 (mttt) cc_final: 0.8061 (mptt) REVERT: D 52 ILE cc_start: 0.9303 (mt) cc_final: 0.8917 (mm) REVERT: F 9 ASN cc_start: 0.9114 (m-40) cc_final: 0.8736 (m-40) REVERT: F 26 CYS cc_start: 0.7779 (m) cc_final: 0.7489 (p) REVERT: F 67 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7855 (tt0) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1024 time to fit residues: 39.8774 Evaluate side-chains 157 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 194 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 chunk 115 optimal weight: 0.0670 chunk 139 optimal weight: 0.7980 chunk 28 optimal weight: 0.0000 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 563 GLN C 639 ASN D 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083759 restraints weight = 30257.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084255 restraints weight = 25194.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085090 restraints weight = 18714.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085490 restraints weight = 15725.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085764 restraints weight = 14236.305| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17430 Z= 0.105 Angle : 0.587 6.789 23475 Z= 0.315 Chirality : 0.049 0.189 2697 Planarity : 0.003 0.058 3012 Dihedral : 6.001 27.659 2241 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.21 (0.17), residues: 2112 helix: -2.36 (0.35), residues: 156 sheet: -1.08 (0.20), residues: 702 loop : -2.87 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 564 TYR 0.009 0.001 TYR E 712 PHE 0.008 0.001 PHE A 658 TRP 0.018 0.001 TRP A 236 HIS 0.005 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00232 (17430) covalent geometry : angle 0.58652 (23475) hydrogen bonds : bond 0.02592 ( 333) hydrogen bonds : angle 5.13232 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9029 (m-30) cc_final: 0.8820 (m-30) REVERT: A 440 LYS cc_start: 0.7410 (mptt) cc_final: 0.6778 (tptp) REVERT: A 779 MET cc_start: 0.8612 (tpp) cc_final: 0.8288 (ttt) REVERT: E 225 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7948 (mt-10) REVERT: E 226 VAL cc_start: 0.9523 (t) cc_final: 0.9265 (p) REVERT: E 263 ASP cc_start: 0.7690 (t70) cc_final: 0.7338 (t70) REVERT: E 454 LEU cc_start: 0.9291 (tp) cc_final: 0.9058 (tp) REVERT: E 506 ILE cc_start: 0.8708 (mt) cc_final: 0.8402 (tt) REVERT: E 522 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6834 (mm-30) REVERT: E 544 ASP cc_start: 0.7802 (m-30) cc_final: 0.7406 (m-30) REVERT: B 9 ASN cc_start: 0.9072 (m-40) cc_final: 0.8852 (t0) REVERT: B 29 LYS cc_start: 0.8739 (mttt) cc_final: 0.8111 (mptt) REVERT: B 42 GLU cc_start: 0.7321 (pp20) cc_final: 0.6930 (tm-30) REVERT: B 83 LYS cc_start: 0.7520 (mttt) cc_final: 0.7317 (tttt) REVERT: D 29 LYS cc_start: 0.8743 (mttt) cc_final: 0.8016 (mptt) REVERT: D 52 ILE cc_start: 0.9319 (mt) cc_final: 0.9024 (mm) REVERT: F 9 ASN cc_start: 0.8937 (m-40) cc_final: 0.8665 (m-40) REVERT: F 29 LYS cc_start: 0.8833 (mttt) cc_final: 0.8177 (mptt) REVERT: F 67 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7776 (tt0) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1054 time to fit residues: 44.1109 Evaluate side-chains 161 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 83 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 GLN C 563 GLN C 611 ASN C 639 ASN E 211 HIS E 370 ASN D 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081316 restraints weight = 31326.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.081937 restraints weight = 26038.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082286 restraints weight = 20599.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.082728 restraints weight = 18170.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082980 restraints weight = 16425.837| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17430 Z= 0.177 Angle : 0.641 7.185 23475 Z= 0.343 Chirality : 0.050 0.179 2697 Planarity : 0.003 0.062 3012 Dihedral : 6.225 27.744 2241 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.20 (0.17), residues: 2112 helix: -2.16 (0.36), residues: 156 sheet: -1.13 (0.20), residues: 723 loop : -2.87 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 564 TYR 0.014 0.001 TYR A 549 PHE 0.017 0.002 PHE C 449 TRP 0.010 0.001 TRP E 236 HIS 0.005 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00410 (17430) covalent geometry : angle 0.64119 (23475) hydrogen bonds : bond 0.02868 ( 333) hydrogen bonds : angle 5.19489 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 254 LEU cc_start: 0.8246 (mt) cc_final: 0.8020 (mt) REVERT: C 263 ASP cc_start: 0.8009 (t70) cc_final: 0.7727 (t70) REVERT: C 567 LEU cc_start: 0.9331 (mt) cc_final: 0.8647 (mt) REVERT: C 756 ILE cc_start: 0.9406 (mp) cc_final: 0.8837 (tp) REVERT: E 225 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 226 VAL cc_start: 0.9528 (t) cc_final: 0.9316 (p) REVERT: E 263 ASP cc_start: 0.7653 (t70) cc_final: 0.7360 (t70) REVERT: E 330 LEU cc_start: 0.9399 (tp) cc_final: 0.9152 (tp) REVERT: E 390 ASP cc_start: 0.9037 (m-30) cc_final: 0.8778 (m-30) REVERT: E 440 LYS cc_start: 0.7158 (mttt) cc_final: 0.6892 (tmtt) REVERT: E 454 LEU cc_start: 0.9325 (tp) cc_final: 0.9066 (tp) REVERT: E 506 ILE cc_start: 0.8775 (mt) cc_final: 0.8432 (tt) REVERT: B 9 ASN cc_start: 0.9033 (m-40) cc_final: 0.8785 (t0) REVERT: B 29 LYS cc_start: 0.8854 (mttt) cc_final: 0.8284 (mptt) REVERT: B 83 LYS cc_start: 0.7700 (mttt) cc_final: 0.7452 (tttt) REVERT: D 29 LYS cc_start: 0.8800 (mttt) cc_final: 0.8134 (mptt) REVERT: D 52 ILE cc_start: 0.9365 (mt) cc_final: 0.9053 (mm) REVERT: D 67 GLU cc_start: 0.7712 (tt0) cc_final: 0.7436 (tt0) REVERT: F 9 ASN cc_start: 0.9061 (m-40) cc_final: 0.8791 (m-40) REVERT: F 42 GLU cc_start: 0.7547 (pp20) cc_final: 0.7280 (tm-30) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.0996 time to fit residues: 35.3945 Evaluate side-chains 146 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 165 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 101 optimal weight: 0.0070 chunk 197 optimal weight: 2.9990 chunk 174 optimal weight: 0.0170 chunk 88 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN C 211 HIS C 563 GLN C 639 ASN E 740 GLN F 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080914 restraints weight = 31284.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.081608 restraints weight = 25168.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082355 restraints weight = 18613.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082829 restraints weight = 15964.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083104 restraints weight = 14211.529| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17430 Z= 0.143 Angle : 0.618 7.143 23475 Z= 0.328 Chirality : 0.049 0.185 2697 Planarity : 0.003 0.062 3012 Dihedral : 6.035 27.073 2241 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.08 (0.17), residues: 2112 helix: -2.05 (0.37), residues: 156 sheet: -1.04 (0.20), residues: 729 loop : -2.81 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 564 TYR 0.008 0.001 TYR E 712 PHE 0.015 0.001 PHE E 357 TRP 0.017 0.001 TRP A 236 HIS 0.007 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00326 (17430) covalent geometry : angle 0.61762 (23475) hydrogen bonds : bond 0.02674 ( 333) hydrogen bonds : angle 5.06400 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.8165 (m-80) cc_final: 0.7924 (m-80) REVERT: C 263 ASP cc_start: 0.8150 (t70) cc_final: 0.7711 (t70) REVERT: E 225 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7977 (mt-10) REVERT: E 226 VAL cc_start: 0.9518 (t) cc_final: 0.9300 (p) REVERT: E 263 ASP cc_start: 0.7694 (t70) cc_final: 0.7402 (t70) REVERT: E 390 ASP cc_start: 0.9063 (m-30) cc_final: 0.8821 (m-30) REVERT: E 454 LEU cc_start: 0.9201 (tp) cc_final: 0.8933 (tp) REVERT: E 506 ILE cc_start: 0.8792 (mt) cc_final: 0.8443 (tt) REVERT: B 29 LYS cc_start: 0.8811 (mttt) cc_final: 0.8141 (mptt) REVERT: B 83 LYS cc_start: 0.7544 (mttt) cc_final: 0.7268 (tttt) REVERT: D 29 LYS cc_start: 0.8777 (mttt) cc_final: 0.8079 (mptt) REVERT: D 52 ILE cc_start: 0.9329 (mt) cc_final: 0.9016 (mm) REVERT: F 9 ASN cc_start: 0.9034 (m-40) cc_final: 0.8782 (m-40) REVERT: F 29 LYS cc_start: 0.8777 (mttt) cc_final: 0.8144 (mptt) REVERT: F 42 GLU cc_start: 0.7590 (pp20) cc_final: 0.7365 (tm-30) REVERT: F 67 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7824 (tt0) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.0989 time to fit residues: 35.8126 Evaluate side-chains 147 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.5980 chunk 172 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 639 ASN E 211 HIS E 563 GLN D 118 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.080476 restraints weight = 31725.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081178 restraints weight = 24601.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081770 restraints weight = 19065.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082146 restraints weight = 16502.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082400 restraints weight = 15017.052| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17430 Z= 0.155 Angle : 0.629 7.104 23475 Z= 0.333 Chirality : 0.050 0.178 2697 Planarity : 0.003 0.066 3012 Dihedral : 6.077 27.101 2241 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer: Outliers : 0.05 % Allowed : 1.22 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.04 (0.17), residues: 2112 helix: -2.00 (0.37), residues: 156 sheet: -1.05 (0.20), residues: 723 loop : -2.75 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 564 TYR 0.013 0.001 TYR E 692 PHE 0.015 0.001 PHE E 326 TRP 0.013 0.001 TRP A 236 HIS 0.007 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00357 (17430) covalent geometry : angle 0.62885 (23475) hydrogen bonds : bond 0.02760 ( 333) hydrogen bonds : angle 5.02508 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7882 (pt0) cc_final: 0.7581 (pt0) REVERT: A 436 ASP cc_start: 0.7937 (t0) cc_final: 0.7625 (t0) REVERT: C 263 ASP cc_start: 0.8066 (t70) cc_final: 0.7704 (t70) REVERT: E 225 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8016 (mt-10) REVERT: E 226 VAL cc_start: 0.9542 (t) cc_final: 0.9330 (p) REVERT: E 263 ASP cc_start: 0.7740 (t70) cc_final: 0.7404 (t70) REVERT: E 330 LEU cc_start: 0.9358 (tp) cc_final: 0.9085 (tp) REVERT: E 390 ASP cc_start: 0.9091 (m-30) cc_final: 0.8840 (m-30) REVERT: E 506 ILE cc_start: 0.8791 (mt) cc_final: 0.8450 (tt) REVERT: B 29 LYS cc_start: 0.8788 (mttt) cc_final: 0.8194 (mptt) REVERT: D 29 LYS cc_start: 0.8750 (mttt) cc_final: 0.8091 (mptt) REVERT: D 52 ILE cc_start: 0.9250 (mt) cc_final: 0.8899 (mm) REVERT: D 67 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8200 (tm-30) REVERT: F 29 LYS cc_start: 0.8781 (mttt) cc_final: 0.8191 (mptt) REVERT: F 42 GLU cc_start: 0.7649 (pp20) cc_final: 0.7410 (tm-30) REVERT: F 67 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7821 (tt0) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.0985 time to fit residues: 31.8989 Evaluate side-chains 144 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 19 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN C 211 HIS C 303 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN E 378 GLN E 460 ASN E 545 ASN E 563 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.074313 restraints weight = 33754.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075864 restraints weight = 22171.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.076950 restraints weight = 16566.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077649 restraints weight = 13399.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078216 restraints weight = 11517.638| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 17430 Z= 0.319 Angle : 0.800 8.306 23475 Z= 0.422 Chirality : 0.054 0.230 2697 Planarity : 0.004 0.069 3012 Dihedral : 7.062 29.648 2241 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.48 % Favored : 83.52 % Rotamer: Outliers : 0.05 % Allowed : 0.61 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.42 (0.17), residues: 2112 helix: -2.04 (0.38), residues: 156 sheet: -1.49 (0.20), residues: 669 loop : -2.87 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 478 TYR 0.014 0.002 TYR C 549 PHE 0.019 0.002 PHE A 357 TRP 0.011 0.002 TRP A 236 HIS 0.008 0.002 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00733 (17430) covalent geometry : angle 0.79995 (23475) hydrogen bonds : bond 0.03548 ( 333) hydrogen bonds : angle 5.58811 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7874 (pt0) cc_final: 0.7634 (pt0) REVERT: A 779 MET cc_start: 0.8891 (ttt) cc_final: 0.8689 (ttt) REVERT: C 225 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8017 (mt-10) REVERT: C 226 VAL cc_start: 0.9505 (t) cc_final: 0.9170 (p) REVERT: C 390 ASP cc_start: 0.9059 (m-30) cc_final: 0.8842 (m-30) REVERT: C 749 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 225 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8034 (mt-10) REVERT: E 226 VAL cc_start: 0.9531 (t) cc_final: 0.9320 (p) REVERT: E 328 ASP cc_start: 0.8469 (p0) cc_final: 0.8238 (p0) REVERT: E 330 LEU cc_start: 0.9385 (tp) cc_final: 0.9158 (tp) REVERT: E 390 ASP cc_start: 0.9120 (m-30) cc_final: 0.8869 (m-30) REVERT: E 506 ILE cc_start: 0.8907 (mt) cc_final: 0.8587 (tt) REVERT: B 9 ASN cc_start: 0.9035 (m-40) cc_final: 0.8556 (t0) REVERT: D 29 LYS cc_start: 0.8926 (mttt) cc_final: 0.8179 (mptt) REVERT: D 52 ILE cc_start: 0.9339 (mt) cc_final: 0.8986 (mm) REVERT: F 9 ASN cc_start: 0.9074 (m-40) cc_final: 0.8804 (m-40) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.1027 time to fit residues: 30.5542 Evaluate side-chains 120 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 196 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 611 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 639 ASN E 192 ASN E 211 HIS E 378 GLN E 563 GLN D 51 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082829 restraints weight = 29484.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083784 restraints weight = 22524.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084529 restraints weight = 18610.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084998 restraints weight = 16027.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085402 restraints weight = 14324.407| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17430 Z= 0.128 Angle : 0.630 7.506 23475 Z= 0.335 Chirality : 0.050 0.274 2697 Planarity : 0.003 0.065 3012 Dihedral : 6.223 28.289 2241 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 0.10 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -3.20 (0.17), residues: 2112 helix: -1.97 (0.38), residues: 156 sheet: -1.31 (0.20), residues: 693 loop : -2.75 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 564 TYR 0.009 0.001 TYR E 560 PHE 0.013 0.001 PHE A 357 TRP 0.014 0.001 TRP A 236 HIS 0.008 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00290 (17430) covalent geometry : angle 0.63046 (23475) hydrogen bonds : bond 0.02563 ( 333) hydrogen bonds : angle 5.05666 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.7837 (pt0) cc_final: 0.7617 (pt0) REVERT: A 548 ASN cc_start: 0.8682 (m-40) cc_final: 0.8272 (p0) REVERT: C 226 VAL cc_start: 0.9477 (t) cc_final: 0.9245 (p) REVERT: C 263 ASP cc_start: 0.7875 (t70) cc_final: 0.7546 (t70) REVERT: C 749 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 225 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7951 (mt-10) REVERT: E 330 LEU cc_start: 0.9286 (tp) cc_final: 0.9048 (tp) REVERT: E 390 ASP cc_start: 0.9116 (m-30) cc_final: 0.8855 (m-30) REVERT: E 506 ILE cc_start: 0.8776 (mt) cc_final: 0.8434 (tt) REVERT: D 29 LYS cc_start: 0.8882 (mttt) cc_final: 0.8267 (mptt) REVERT: D 52 ILE cc_start: 0.9424 (mt) cc_final: 0.9116 (mm) REVERT: F 42 GLU cc_start: 0.7490 (pp20) cc_final: 0.7130 (tm-30) REVERT: F 67 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7739 (tt0) outliers start: 2 outliers final: 2 residues processed: 200 average time/residue: 0.0979 time to fit residues: 31.7504 Evaluate side-chains 139 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 162 optimal weight: 0.0670 chunk 124 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 0.0170 chunk 133 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 150 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 GLN C 718 ASN E 563 GLN B 118 GLN F 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084616 restraints weight = 30289.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085039 restraints weight = 24377.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.085530 restraints weight = 19718.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085968 restraints weight = 16395.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086311 restraints weight = 14668.756| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17430 Z= 0.099 Angle : 0.600 10.399 23475 Z= 0.317 Chirality : 0.050 0.248 2697 Planarity : 0.003 0.066 3012 Dihedral : 5.606 26.048 2241 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -2.87 (0.18), residues: 2112 helix: -1.58 (0.40), residues: 138 sheet: -1.10 (0.20), residues: 702 loop : -2.53 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 730 TYR 0.024 0.001 TYR A 656 PHE 0.015 0.001 PHE C 521 TRP 0.011 0.001 TRP A 236 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00215 (17430) covalent geometry : angle 0.60003 (23475) hydrogen bonds : bond 0.02262 ( 333) hydrogen bonds : angle 4.77241 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.19 seconds wall clock time: 38 minutes 54.31 seconds (2334.31 seconds total)