Starting phenix.real_space_refine on Thu Feb 5 05:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddc_46765/02_2026/9ddc_46765.map" } resolution = 2.9 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= 0.002 sd= 0.014 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 66 5.16 5 C 9294 2.51 5 N 2583 2.21 5 O 2811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14754 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4848 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 571} Chain breaks: 1 Chain: "B" Number of atoms: 4848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4848 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 571} Chain breaks: 1 Chain: "C" Number of atoms: 4848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4848 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 571} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.11, per 1000 atoms: 0.21 Number of scatterers: 14754 At special positions: 0 Unit cell: (100.43, 94.62, 179.28, 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 66 16.00 O 2811 8.00 N 2583 7.00 C 9294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 141 " " NAG A 902 " - " ASN A 430 " " NAG A 903 " - " ASN A 674 " " NAG B 901 " - " ASN B 141 " " NAG B 902 " - " ASN B 430 " " NAG B 903 " - " ASN B 674 " " NAG C 901 " - " ASN C 141 " " NAG C 902 " - " ASN C 430 " " NAG C 903 " - " ASN C 674 " " NAG D 1 " - " ASN A 398 " " NAG E 1 " - " ASN B 398 " " NAG F 1 " - " ASN C 398 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 555.4 milliseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 25.5% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 410 through 428 removed outlier: 4.593A pdb=" N GLY A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 removed outlier: 5.799A pdb=" N GLU A 462 " --> pdb=" O THR A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 463 through 473 removed outlier: 4.271A pdb=" N LEU A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 Proline residue: A 516 - end of helix removed outlier: 4.421A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 410 through 428 removed outlier: 4.410A pdb=" N GLY B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 462 removed outlier: 5.799A pdb=" N GLU B 462 " --> pdb=" O THR B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 459 through 462' Processing helix chain 'B' and resid 463 through 473 removed outlier: 4.272A pdb=" N LEU B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 Proline residue: B 516 - end of helix removed outlier: 4.421A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 711 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 410 through 428 removed outlier: 4.410A pdb=" N GLY C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 462 removed outlier: 5.799A pdb=" N GLU C 462 " --> pdb=" O THR C 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 462' Processing helix chain 'C' and resid 463 through 473 removed outlier: 4.272A pdb=" N LEU C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 Proline residue: C 516 - end of helix removed outlier: 4.420A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 711 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.477A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 564 removed outlier: 3.512A pdb=" N ARG A 562 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 124 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL B 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN A 126 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 191 removed outlier: 5.451A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.344A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 324 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.586A pdb=" N ARG A 639 " --> pdb=" O PHE A 650 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLN A 658 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR A 649 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 667 removed outlier: 4.065A pdb=" N THR A 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 567 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 562 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.476A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 559 through 564 removed outlier: 3.511A pdb=" N ARG B 562 " --> pdb=" O ALA B 569 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 667 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLN B 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 180 through 191 removed outlier: 5.452A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.345A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC2, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC3, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.587A pdb=" N ARG B 639 " --> pdb=" O PHE B 650 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLN B 658 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR B 649 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.476A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.723A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 180 through 191 removed outlier: 5.451A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.345A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 324 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD3, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD4, first strand: chain 'C' and resid 375 through 379 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.586A pdb=" N ARG C 639 " --> pdb=" O PHE C 650 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TYR C 647 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLN C 658 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR C 649 " --> pdb=" O SER C 656 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4868 1.34 - 1.46: 3353 1.46 - 1.58: 6791 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 15114 Sorted by residual: bond pdb=" N ILE B 582 " pdb=" CA ILE B 582 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.93e+00 bond pdb=" N ILE C 675 " pdb=" CA ILE C 675 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.62e+00 bond pdb=" N ILE B 675 " pdb=" CA ILE B 675 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.60e+00 bond pdb=" N ILE B 589 " pdb=" CA ILE B 589 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.15e-02 7.56e+03 9.56e+00 bond pdb=" N ILE A 675 " pdb=" CA ILE A 675 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.25e-02 6.40e+03 9.53e+00 ... (remaining 15109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 19010 1.27 - 2.53: 1201 2.53 - 3.80: 227 3.80 - 5.06: 81 5.06 - 6.33: 16 Bond angle restraints: 20535 Sorted by residual: angle pdb=" N MET A 587 " pdb=" CA MET A 587 " pdb=" C MET A 587 " ideal model delta sigma weight residual 113.17 108.07 5.10 1.26e+00 6.30e-01 1.64e+01 angle pdb=" N THR C 332 " pdb=" CA THR C 332 " pdb=" C THR C 332 " ideal model delta sigma weight residual 109.46 103.20 6.26 1.66e+00 3.63e-01 1.42e+01 angle pdb=" CA LEU C 673 " pdb=" C LEU C 673 " pdb=" O LEU C 673 " ideal model delta sigma weight residual 120.70 116.63 4.07 1.08e+00 8.57e-01 1.42e+01 angle pdb=" N THR A 332 " pdb=" CA THR A 332 " pdb=" C THR A 332 " ideal model delta sigma weight residual 109.46 103.21 6.25 1.66e+00 3.63e-01 1.42e+01 angle pdb=" N THR B 332 " pdb=" CA THR B 332 " pdb=" C THR B 332 " ideal model delta sigma weight residual 109.46 103.23 6.23 1.66e+00 3.63e-01 1.41e+01 ... (remaining 20530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 8482 17.40 - 34.79: 565 34.79 - 52.19: 133 52.19 - 69.59: 33 69.59 - 86.99: 21 Dihedral angle restraints: 9234 sinusoidal: 3927 harmonic: 5307 Sorted by residual: dihedral pdb=" CA ASP C 389 " pdb=" CB ASP C 389 " pdb=" CG ASP C 389 " pdb=" OD1 ASP C 389 " ideal model delta sinusoidal sigma weight residual -30.00 -88.30 58.30 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " pdb=" CG ASP A 389 " pdb=" OD1 ASP A 389 " ideal model delta sinusoidal sigma weight residual -30.00 -88.30 58.30 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP B 389 " pdb=" CB ASP B 389 " pdb=" CG ASP B 389 " pdb=" OD1 ASP B 389 " ideal model delta sinusoidal sigma weight residual -30.00 -88.29 58.29 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 9231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1592 0.041 - 0.083: 433 0.083 - 0.124: 196 0.124 - 0.165: 36 0.165 - 0.207: 14 Chirality restraints: 2271 Sorted by residual: chirality pdb=" CA VAL B 613 " pdb=" N VAL B 613 " pdb=" C VAL B 613 " pdb=" CB VAL B 613 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 582 " pdb=" N ILE B 582 " pdb=" C ILE B 582 " pdb=" CB ILE B 582 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A 583 " pdb=" N VAL A 583 " pdb=" C VAL A 583 " pdb=" CB VAL A 583 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2268 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 592 " -0.205 9.50e-02 1.11e+02 9.18e-02 5.17e+00 pdb=" NE ARG C 592 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 592 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 592 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 592 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 258 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C ARG B 258 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG B 258 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 259 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 258 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ARG A 258 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG A 258 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 259 " 0.010 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2734 2.77 - 3.31: 13523 3.31 - 3.84: 23791 3.84 - 4.37: 28789 4.37 - 4.90: 51068 Nonbonded interactions: 119905 Sorted by model distance: nonbonded pdb=" OG1 THR A 498 " pdb=" OE2 GLU B 687 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 498 " pdb=" OE2 GLU C 687 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU A 687 " pdb=" OG1 THR C 498 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU B 535 " pdb=" OE1 GLU C 535 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU A 535 " pdb=" OE2 GLU C 535 " model vdw 2.328 3.040 ... (remaining 119900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 : 0.005 0.039 15144 Z= 0.286 Angle : 0.762 6.330 20610 Z= 0.470 Chirality : 0.050 0.207 2271 Planarity : 0.005 0.092 2664 Dihedral : 12.950 86.986 5775 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.20), residues: 1788 helix: 0.64 (0.29), residues: 327 sheet: -0.98 (0.21), residues: 543 loop : -0.32 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 132 TYR 0.013 0.001 TYR B 296 PHE 0.010 0.001 PHE C 604 TRP 0.002 0.001 TRP C 247 HIS 0.005 0.001 HIS B 433 Details of bonding type rmsd covalent geometry : bond 0.00453 (15114) covalent geometry : angle 0.75736 (20535) SS BOND : bond 0.00235 ( 15) SS BOND : angle 0.81852 ( 30) hydrogen bonds : bond 0.19445 ( 563) hydrogen bonds : angle 9.22708 ( 1785) link_BETA1-4 : bond 0.00488 ( 3) link_BETA1-4 : angle 2.58348 ( 9) link_NAG-ASN : bond 0.00171 ( 12) link_NAG-ASN : angle 1.76842 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.540 Fit side-chains REVERT: C 643 PHE cc_start: 0.8935 (t80) cc_final: 0.8644 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.7334 time to fit residues: 51.2335 Evaluate side-chains 57 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 433 HIS A 534 HIS B 248 HIS B 433 HIS B 534 HIS C 248 HIS C 433 HIS C 534 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.046545 restraints weight = 35362.506| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.08 r_work: 0.2506 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15144 Z= 0.262 Angle : 0.570 9.072 20610 Z= 0.303 Chirality : 0.045 0.170 2271 Planarity : 0.004 0.044 2664 Dihedral : 3.551 19.615 2358 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.28 % Allowed : 8.37 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1788 helix: 0.99 (0.28), residues: 333 sheet: -0.51 (0.20), residues: 579 loop : -0.16 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 605 TYR 0.016 0.002 TYR A 164 PHE 0.014 0.002 PHE A 643 TRP 0.007 0.001 TRP B 174 HIS 0.008 0.002 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00624 (15114) covalent geometry : angle 0.55386 (20535) SS BOND : bond 0.00260 ( 15) SS BOND : angle 2.97143 ( 30) hydrogen bonds : bond 0.04941 ( 563) hydrogen bonds : angle 6.23488 ( 1785) link_BETA1-4 : bond 0.00138 ( 3) link_BETA1-4 : angle 2.06516 ( 9) link_NAG-ASN : bond 0.00245 ( 12) link_NAG-ASN : angle 1.52350 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.529 Fit side-chains REVERT: A 421 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7616 (mpp) REVERT: A 605 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8040 (ptp90) REVERT: B 421 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8323 (mtt) REVERT: B 587 MET cc_start: 0.7654 (pmm) cc_final: 0.7213 (pmm) REVERT: B 724 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.8020 (p90) REVERT: C 421 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7668 (mpp) REVERT: C 587 MET cc_start: 0.8343 (pmm) cc_final: 0.7835 (pmm) REVERT: C 643 PHE cc_start: 0.9046 (t80) cc_final: 0.8789 (t80) outliers start: 20 outliers final: 7 residues processed: 74 average time/residue: 0.5981 time to fit residues: 49.0537 Evaluate side-chains 68 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.045289 restraints weight = 35702.689| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.12 r_work: 0.2474 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 15144 Z= 0.310 Angle : 0.559 7.863 20610 Z= 0.297 Chirality : 0.045 0.178 2271 Planarity : 0.004 0.044 2664 Dihedral : 4.001 23.676 2358 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.43 % Allowed : 8.37 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1788 helix: 1.12 (0.29), residues: 333 sheet: -0.23 (0.20), residues: 579 loop : -0.35 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 605 TYR 0.013 0.001 TYR B 164 PHE 0.025 0.002 PHE B 643 TRP 0.007 0.001 TRP B 174 HIS 0.006 0.001 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00733 (15114) covalent geometry : angle 0.54566 (20535) SS BOND : bond 0.00487 ( 15) SS BOND : angle 2.59392 ( 30) hydrogen bonds : bond 0.04683 ( 563) hydrogen bonds : angle 5.86173 ( 1785) link_BETA1-4 : bond 0.00095 ( 3) link_BETA1-4 : angle 1.93731 ( 9) link_NAG-ASN : bond 0.00317 ( 12) link_NAG-ASN : angle 1.61538 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 55 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7661 (mpp) REVERT: A 605 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8022 (ptp90) REVERT: A 724 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7920 (p90) REVERT: B 421 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: B 587 MET cc_start: 0.7885 (pmm) cc_final: 0.7521 (pmm) REVERT: B 607 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: B 724 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7985 (p90) REVERT: C 421 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: C 587 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8024 (pmm) REVERT: C 643 PHE cc_start: 0.9177 (t80) cc_final: 0.8951 (t80) REVERT: C 724 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7935 (p90) outliers start: 38 outliers final: 13 residues processed: 87 average time/residue: 0.5355 time to fit residues: 51.9471 Evaluate side-chains 77 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 724 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 110 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 255 ASN C 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.072810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.047243 restraints weight = 35328.710| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.09 r_work: 0.2522 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15144 Z= 0.115 Angle : 0.481 9.523 20610 Z= 0.256 Chirality : 0.041 0.173 2271 Planarity : 0.003 0.039 2664 Dihedral : 3.898 22.971 2358 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.92 % Allowed : 9.07 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1788 helix: 1.26 (0.29), residues: 333 sheet: 0.09 (0.20), residues: 564 loop : -0.37 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 132 TYR 0.013 0.001 TYR C 165 PHE 0.017 0.001 PHE B 643 TRP 0.007 0.001 TRP A 528 HIS 0.005 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00256 (15114) covalent geometry : angle 0.46028 (20535) SS BOND : bond 0.00559 ( 15) SS BOND : angle 3.34251 ( 30) hydrogen bonds : bond 0.03689 ( 563) hydrogen bonds : angle 5.37237 ( 1785) link_BETA1-4 : bond 0.00297 ( 3) link_BETA1-4 : angle 1.61040 ( 9) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.22512 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 56 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8835 (t70) REVERT: A 587 MET cc_start: 0.8148 (pmm) cc_final: 0.7397 (pmm) REVERT: B 167 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8917 (m-30) REVERT: B 534 HIS cc_start: 0.9113 (OUTLIER) cc_final: 0.8763 (t70) REVERT: B 587 MET cc_start: 0.7873 (pmm) cc_final: 0.7446 (pmm) REVERT: B 724 HIS cc_start: 0.8472 (OUTLIER) cc_final: 0.8018 (p90) REVERT: C 534 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (t70) REVERT: C 587 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7984 (pmm) REVERT: C 643 PHE cc_start: 0.9141 (t80) cc_final: 0.8899 (t80) outliers start: 30 outliers final: 10 residues processed: 80 average time/residue: 0.6104 time to fit residues: 54.0810 Evaluate side-chains 72 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 HIS C 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.047187 restraints weight = 35306.345| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.09 r_work: 0.2524 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15144 Z= 0.140 Angle : 0.473 9.393 20610 Z= 0.251 Chirality : 0.041 0.169 2271 Planarity : 0.003 0.037 2664 Dihedral : 3.860 22.264 2358 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.72 % Allowed : 9.26 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1788 helix: 1.32 (0.29), residues: 333 sheet: 0.09 (0.21), residues: 582 loop : -0.26 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.010 0.001 TYR B 649 PHE 0.019 0.001 PHE B 643 TRP 0.006 0.001 TRP C 174 HIS 0.004 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00328 (15114) covalent geometry : angle 0.45380 (20535) SS BOND : bond 0.00402 ( 15) SS BOND : angle 3.14969 ( 30) hydrogen bonds : bond 0.03597 ( 563) hydrogen bonds : angle 5.22897 ( 1785) link_BETA1-4 : bond 0.00116 ( 3) link_BETA1-4 : angle 1.52974 ( 9) link_NAG-ASN : bond 0.00224 ( 12) link_NAG-ASN : angle 1.24499 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.9131 (OUTLIER) cc_final: 0.8796 (t70) REVERT: A 587 MET cc_start: 0.8184 (pmm) cc_final: 0.7725 (pmm) REVERT: A 724 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.7914 (p90) REVERT: B 167 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8889 (m-30) REVERT: B 587 MET cc_start: 0.8048 (pmm) cc_final: 0.7571 (pmm) REVERT: B 724 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.8041 (p90) REVERT: C 167 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8829 (m-30) REVERT: C 534 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8741 (t70) REVERT: C 587 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7944 (pmm) REVERT: C 643 PHE cc_start: 0.9158 (t80) cc_final: 0.8934 (t80) REVERT: C 724 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7920 (p90) outliers start: 27 outliers final: 11 residues processed: 84 average time/residue: 0.6693 time to fit residues: 61.9499 Evaluate side-chains 76 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 724 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 97 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 142 optimal weight: 0.0040 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.046078 restraints weight = 35207.065| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.06 r_work: 0.2494 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15144 Z= 0.215 Angle : 0.496 8.706 20610 Z= 0.263 Chirality : 0.043 0.171 2271 Planarity : 0.003 0.039 2664 Dihedral : 4.018 23.415 2358 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 9.77 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1788 helix: 1.36 (0.29), residues: 333 sheet: 0.11 (0.21), residues: 582 loop : -0.31 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.011 0.001 TYR B 164 PHE 0.021 0.001 PHE A 643 TRP 0.006 0.001 TRP C 174 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00510 (15114) covalent geometry : angle 0.47936 (20535) SS BOND : bond 0.00326 ( 15) SS BOND : angle 3.00097 ( 30) hydrogen bonds : bond 0.03889 ( 563) hydrogen bonds : angle 5.30357 ( 1785) link_BETA1-4 : bond 0.00166 ( 3) link_BETA1-4 : angle 1.57664 ( 9) link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 1.38833 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8906 (t70) REVERT: A 535 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8409 (mm-30) REVERT: A 587 MET cc_start: 0.8219 (pmm) cc_final: 0.7748 (pmm) REVERT: A 724 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.7921 (p90) REVERT: B 132 ARG cc_start: 0.8238 (ttp80) cc_final: 0.8010 (ttp80) REVERT: B 167 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8922 (m-30) REVERT: B 587 MET cc_start: 0.8104 (pmm) cc_final: 0.7771 (pmm) REVERT: B 724 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8033 (p90) REVERT: C 167 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: C 534 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8819 (t70) REVERT: C 587 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7948 (pmm) REVERT: C 643 PHE cc_start: 0.9201 (t80) cc_final: 0.8984 (t80) REVERT: C 724 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7931 (p90) outliers start: 32 outliers final: 14 residues processed: 85 average time/residue: 0.6183 time to fit residues: 58.3617 Evaluate side-chains 80 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 724 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.072314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.046832 restraints weight = 34939.088| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.06 r_work: 0.2517 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15144 Z= 0.150 Angle : 0.460 7.039 20610 Z= 0.245 Chirality : 0.041 0.170 2271 Planarity : 0.003 0.037 2664 Dihedral : 3.974 23.345 2358 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.98 % Allowed : 10.34 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1788 helix: 1.43 (0.29), residues: 333 sheet: 0.19 (0.21), residues: 582 loop : -0.29 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.009 0.001 TYR B 164 PHE 0.016 0.001 PHE B 643 TRP 0.006 0.001 TRP C 539 HIS 0.005 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00351 (15114) covalent geometry : angle 0.44774 (20535) SS BOND : bond 0.00319 ( 15) SS BOND : angle 2.37407 ( 30) hydrogen bonds : bond 0.03595 ( 563) hydrogen bonds : angle 5.16977 ( 1785) link_BETA1-4 : bond 0.00173 ( 3) link_BETA1-4 : angle 1.43888 ( 9) link_NAG-ASN : bond 0.00250 ( 12) link_NAG-ASN : angle 1.25539 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8184 (pmm) cc_final: 0.7767 (pmm) REVERT: A 724 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7949 (p90) REVERT: B 132 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7908 (ttp80) REVERT: B 587 MET cc_start: 0.8084 (pmm) cc_final: 0.7814 (pmm) REVERT: B 724 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.8007 (p90) REVERT: C 167 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8885 (m-30) REVERT: C 587 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7930 (pmm) REVERT: C 643 PHE cc_start: 0.9190 (t80) cc_final: 0.8966 (t80) REVERT: C 724 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7927 (p90) outliers start: 31 outliers final: 14 residues processed: 85 average time/residue: 0.6224 time to fit residues: 58.7129 Evaluate side-chains 74 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 724 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 147 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS C 534 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.072065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.046785 restraints weight = 35545.383| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.05 r_work: 0.2508 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15144 Z= 0.160 Angle : 0.465 6.828 20610 Z= 0.248 Chirality : 0.041 0.169 2271 Planarity : 0.003 0.037 2664 Dihedral : 3.981 23.259 2358 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.66 % Allowed : 10.92 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 1788 helix: 1.44 (0.29), residues: 333 sheet: 0.21 (0.21), residues: 582 loop : -0.28 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.010 0.001 TYR B 164 PHE 0.017 0.001 PHE A 643 TRP 0.008 0.001 TRP A 539 HIS 0.008 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00377 (15114) covalent geometry : angle 0.45399 (20535) SS BOND : bond 0.00335 ( 15) SS BOND : angle 2.27698 ( 30) hydrogen bonds : bond 0.03611 ( 563) hydrogen bonds : angle 5.15012 ( 1785) link_BETA1-4 : bond 0.00124 ( 3) link_BETA1-4 : angle 1.42836 ( 9) link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.27800 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 587 MET cc_start: 0.8159 (pmm) cc_final: 0.7745 (pmm) REVERT: A 724 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.7957 (p90) REVERT: B 132 ARG cc_start: 0.8207 (ttp80) cc_final: 0.7945 (ttp80) REVERT: B 587 MET cc_start: 0.8073 (pmm) cc_final: 0.7754 (pmm) REVERT: B 724 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8065 (p90) REVERT: C 167 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: C 587 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7910 (pmm) REVERT: C 724 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7936 (p90) outliers start: 26 outliers final: 15 residues processed: 83 average time/residue: 0.5835 time to fit residues: 53.8523 Evaluate side-chains 78 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 719 ILE Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 719 ILE Chi-restraints excluded: chain C residue 724 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 25 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 0.0030 chunk 56 optimal weight: 0.0040 chunk 171 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 534 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.072853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.047565 restraints weight = 35543.146| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.09 r_work: 0.2533 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15144 Z= 0.107 Angle : 0.445 5.919 20610 Z= 0.237 Chirality : 0.040 0.167 2271 Planarity : 0.003 0.036 2664 Dihedral : 3.875 22.151 2358 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.53 % Allowed : 11.24 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1788 helix: 1.47 (0.29), residues: 333 sheet: 0.26 (0.21), residues: 582 loop : -0.25 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 132 TYR 0.010 0.001 TYR C 649 PHE 0.009 0.001 PHE C 159 TRP 0.008 0.001 TRP C 539 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00245 (15114) covalent geometry : angle 0.43592 (20535) SS BOND : bond 0.00344 ( 15) SS BOND : angle 1.94906 ( 30) hydrogen bonds : bond 0.03303 ( 563) hydrogen bonds : angle 5.02319 ( 1785) link_BETA1-4 : bond 0.00245 ( 3) link_BETA1-4 : angle 1.31183 ( 9) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 1.14397 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 587 MET cc_start: 0.8181 (pmm) cc_final: 0.7799 (pmm) REVERT: A 605 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8172 (ptp90) REVERT: A 724 HIS cc_start: 0.8433 (OUTLIER) cc_final: 0.7973 (p90) REVERT: B 535 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 587 MET cc_start: 0.8029 (pmm) cc_final: 0.7732 (pmm) REVERT: B 724 HIS cc_start: 0.8467 (OUTLIER) cc_final: 0.8026 (p90) REVERT: C 112 ASN cc_start: 0.9449 (m110) cc_final: 0.8506 (t0) REVERT: C 167 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8879 (m-30) REVERT: C 587 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7849 (pmm) outliers start: 24 outliers final: 11 residues processed: 84 average time/residue: 0.5816 time to fit residues: 54.2405 Evaluate side-chains 76 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 605 ARG Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 0.0370 chunk 135 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.045469 restraints weight = 35705.862| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.06 r_work: 0.2477 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15144 Z= 0.288 Angle : 0.540 9.369 20610 Z= 0.286 Chirality : 0.044 0.172 2271 Planarity : 0.004 0.039 2664 Dihedral : 4.177 24.521 2358 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.15 % Allowed : 11.62 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 1788 helix: 1.39 (0.29), residues: 333 sheet: 0.16 (0.21), residues: 582 loop : -0.36 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 132 TYR 0.013 0.001 TYR B 164 PHE 0.017 0.002 PHE A 643 TRP 0.006 0.001 TRP B 528 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00683 (15114) covalent geometry : angle 0.52076 (20535) SS BOND : bond 0.00416 ( 15) SS BOND : angle 3.38264 ( 30) hydrogen bonds : bond 0.04114 ( 563) hydrogen bonds : angle 5.32623 ( 1785) link_BETA1-4 : bond 0.00136 ( 3) link_BETA1-4 : angle 1.55555 ( 9) link_NAG-ASN : bond 0.00361 ( 12) link_NAG-ASN : angle 1.51263 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 587 MET cc_start: 0.8191 (pmm) cc_final: 0.7670 (pmm) REVERT: A 724 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7987 (p90) REVERT: B 587 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7739 (pmm) REVERT: B 724 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8074 (p90) REVERT: C 112 ASN cc_start: 0.9465 (m110) cc_final: 0.8453 (t0) REVERT: C 167 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8926 (m-30) REVERT: C 587 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7959 (pmm) outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 0.5586 time to fit residues: 47.8975 Evaluate side-chains 74 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 668 SER Chi-restraints excluded: chain A residue 724 HIS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 587 MET Chi-restraints excluded: chain B residue 724 HIS Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 607 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS C 534 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.047007 restraints weight = 35574.415| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.11 r_work: 0.2517 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15144 Z= 0.131 Angle : 0.464 7.563 20610 Z= 0.247 Chirality : 0.041 0.169 2271 Planarity : 0.003 0.037 2664 Dihedral : 4.049 23.782 2358 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.28 % Allowed : 11.49 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1788 helix: 1.41 (0.29), residues: 333 sheet: 0.21 (0.21), residues: 582 loop : -0.34 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 132 TYR 0.009 0.001 TYR B 164 PHE 0.019 0.001 PHE C 643 TRP 0.008 0.001 TRP C 539 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00308 (15114) covalent geometry : angle 0.45066 (20535) SS BOND : bond 0.00331 ( 15) SS BOND : angle 2.50880 ( 30) hydrogen bonds : bond 0.03471 ( 563) hydrogen bonds : angle 5.12372 ( 1785) link_BETA1-4 : bond 0.00218 ( 3) link_BETA1-4 : angle 1.33663 ( 9) link_NAG-ASN : bond 0.00255 ( 12) link_NAG-ASN : angle 1.21144 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.97 seconds wall clock time: 58 minutes 5.11 seconds (3485.11 seconds total)