Starting phenix.real_space_refine on Thu Feb 5 01:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9n_62194/02_2026/9k9n_62194.map" } resolution = 2.61 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= 0.023 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 8851 2.51 5 N 2240 2.21 5 O 2683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s 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: 13840 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5942 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 26, 'TRANS': 698} Chain: "B" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5942 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 26, 'TRANS': 698} Chain: "C" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} 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: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} 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: "I" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.98, per 1000 atoms: 0.22 Number of scatterers: 13840 At special positions: 0 Unit cell: (86.25, 135.24, 143.52, 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 2683 8.00 N 2240 7.00 C 8851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 762 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 394 " distance=2.05 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 472 " distance=2.04 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 445 " - pdb=" SG CYS C 593 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 534 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 92 " " NAG A 802 " - " ASN A 150 " " NAG A 803 " - " ASN A 219 " " NAG A 804 " - " ASN A 229 " " NAG A 805 " - " ASN A 321 " " NAG A 806 " - " ASN A 520 " " NAG B 801 " - " ASN B 92 " " NAG B 802 " - " ASN B 150 " " NAG B 803 " - " ASN B 219 " " NAG B 804 " - " ASN B 520 " " NAG D 1 " - " ASN A 85 " " NAG E 1 " - " ASN A 281 " " NAG F 1 " - " ASN B 85 " " NAG G 1 " - " ASN B 229 " " NAG H 1 " - " ASN B 281 " " NAG I 1 " - " ASN B 321 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 563.4 milliseconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 29 sheets defined 21.7% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 91 through 97 removed outlier: 4.085A pdb=" N PHE A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 497 through 505 removed outlier: 3.522A pdb=" N ASP A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.648A pdb=" N TYR A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 600 through 616 removed outlier: 3.507A pdb=" N GLU A 604 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 607 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 616 " --> pdb=" O GLN A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 658 through 662 removed outlier: 3.691A pdb=" N TYR A 662 " --> pdb=" O TRP A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.574A pdb=" N ARG A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 686 removed outlier: 3.644A pdb=" N ARG A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.673A pdb=" N ALA A 692 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 697 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.351A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 763 removed outlier: 3.672A pdb=" N TYR A 752 " --> pdb=" O HIS A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.061A pdb=" N PHE B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 290 through 295 removed outlier: 4.081A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 562 through 570 removed outlier: 3.631A pdb=" N TYR B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 600 through 615 removed outlier: 3.685A pdb=" N GLU B 604 " --> pdb=" O THR B 600 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 606 " --> pdb=" O GLU B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 658 through 662 removed outlier: 3.711A pdb=" N TYR B 662 " --> pdb=" O TRP B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 671 removed outlier: 3.606A pdb=" N ARG B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 686 Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.763A pdb=" N SER B 690 " --> pdb=" O THR B 687 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 692 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 697 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 4.406A pdb=" N SER B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 719 " --> pdb=" O GLN B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 763 removed outlier: 3.636A pdb=" N TYR B 752 " --> pdb=" O HIS B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.864A pdb=" N LEU C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 443 Processing helix chain 'C' and resid 470 through 475 Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.770A pdb=" N SER C 536 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 537 " --> pdb=" O CYS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 590 removed outlier: 4.243A pdb=" N ASN C 590 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 7.483A pdb=" N LYS A 41 " --> pdb=" O GLN A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.776A pdb=" N ILE A 76 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.796A pdb=" N ASP A 104 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 120 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LYS A 122 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A 127 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.771A pdb=" N TRP A 154 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA7, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.735A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 336 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.735A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.521A pdb=" N PHE A 371 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 410 removed outlier: 6.815A pdb=" N ILE A 418 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE A 407 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR A 416 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA A 409 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR A 414 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 457 through 461 removed outlier: 6.752A pdb=" N LEU A 482 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 493 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N SER A 484 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 491 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 511 through 518 removed outlier: 3.511A pdb=" N VAL A 575 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A 578 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR A 540 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS A 622 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 542 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 624 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 544 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 626 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS A 649 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 624 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ILE A 651 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 626 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 628 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR A 700 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N MET A 733 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 702 " --> pdb=" O MET A 733 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N TYR A 735 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N HIS A 704 " --> pdb=" O TYR A 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 42 removed outlier: 7.370A pdb=" N LYS B 41 " --> pdb=" O GLN B 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.560A pdb=" N ILE B 76 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.925A pdb=" N ASP B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 120 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 129 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 141 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.814A pdb=" N TRP B 154 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.632A pdb=" N ASN B 229 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 265 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.383A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 302 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.383A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 302 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 363 through 364 removed outlier: 3.532A pdb=" N PHE B 371 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 373 " --> pdb=" O CYS B 385 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 404 through 410 removed outlier: 6.784A pdb=" N ILE B 418 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 407 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N TYR B 416 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA B 409 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 414 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 457 through 461 removed outlier: 3.512A pdb=" N GLU B 495 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 482 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 493 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N SER B 484 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU B 491 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 511 through 519 removed outlier: 3.506A pdb=" N VAL B 575 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE B 578 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 540 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LYS B 622 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU B 542 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B 624 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 544 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 626 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 546 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY B 628 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N CYS B 649 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 624 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE B 651 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE B 626 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL B 653 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 628 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR B 700 " --> pdb=" O GLN B 731 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N MET B 733 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 702 " --> pdb=" O MET B 733 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N TYR B 735 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N HIS B 704 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 408 through 413 removed outlier: 3.550A pdb=" N LYS C 408 " --> pdb=" O TYR C 453 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 491 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL C 428 " --> pdb=" O THR C 491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 416 through 417 removed outlier: 3.606A pdb=" N TYR C 417 " --> pdb=" O CYS C 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 522 through 523 removed outlier: 3.527A pdb=" N TYR C 504 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 569 " --> pdb=" O TYR C 504 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 506 " --> pdb=" O ALA C 567 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 565 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS C 510 " --> pdb=" O VAL C 563 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 563 " --> pdb=" O CYS C 510 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG C 512 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 561 " --> pdb=" O ARG C 512 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1212 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: 2.51 Time building geometry restraints manager: 1.79 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: 4295 1.34 - 1.46: 3563 1.46 - 1.58: 6264 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 14222 Sorted by residual: bond pdb=" C LEU A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.34e-02 5.57e+03 1.43e+01 bond pdb=" CA LEU A 477 " pdb=" C LEU A 477 " ideal model delta sigma weight residual 1.528 1.572 -0.044 1.18e-02 7.18e+03 1.36e+01 bond pdb=" CA SER B 473 " pdb=" C SER B 473 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.44e-02 4.82e+03 7.42e+00 bond pdb=" C1 MAN G 4 " pdb=" C2 MAN G 4 " ideal model delta sigma weight residual 1.526 1.570 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 MAN G 5 " pdb=" C2 MAN G 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 14217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 19105 2.13 - 4.27: 206 4.27 - 6.40: 17 6.40 - 8.54: 6 8.54 - 10.67: 2 Bond angle restraints: 19336 Sorted by residual: angle pdb=" N SER B 473 " pdb=" CA SER B 473 " pdb=" C SER B 473 " ideal model delta sigma weight residual 109.54 99.49 10.05 1.37e+00 5.33e-01 5.38e+01 angle pdb=" N GLY A 474 " pdb=" CA GLY A 474 " pdb=" C GLY A 474 " ideal model delta sigma weight residual 112.34 123.01 -10.67 2.04e+00 2.40e-01 2.74e+01 angle pdb=" N PRO A 475 " pdb=" CA PRO A 475 " pdb=" C PRO A 475 " ideal model delta sigma weight residual 113.40 107.37 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" N SER A 473 " pdb=" CA SER A 473 " pdb=" C SER A 473 " ideal model delta sigma weight residual 111.14 106.47 4.67 1.08e+00 8.57e-01 1.87e+01 angle pdb=" N PRO B 478 " pdb=" CA PRO B 478 " pdb=" C PRO B 478 " ideal model delta sigma weight residual 111.15 117.70 -6.55 1.58e+00 4.01e-01 1.72e+01 ... (remaining 19331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 8219 21.86 - 43.73: 386 43.73 - 65.59: 42 65.59 - 87.46: 22 87.46 - 109.32: 8 Dihedral angle restraints: 8677 sinusoidal: 3776 harmonic: 4901 Sorted by residual: dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual 93.00 151.58 -58.58 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CA CYS B 394 " pdb=" C CYS B 394 " pdb=" N THR B 395 " pdb=" CA THR B 395 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 415 " pdb=" CB CYS C 415 " ideal model delta sinusoidal sigma weight residual 93.00 55.30 37.70 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 8674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1994 0.099 - 0.198: 125 0.198 - 0.298: 2 0.298 - 0.397: 1 0.397 - 0.496: 1 Chirality restraints: 2123 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 85 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" C1 NAG A 805 " pdb=" ND2 ASN A 321 " pdb=" C2 NAG A 805 " pdb=" O5 NAG A 805 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2120 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 229 " -0.003 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" CG ASN B 229 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 229 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B 229 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 474 " -0.051 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO A 475 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 627 " 0.013 2.00e-02 2.50e+03 1.48e-02 5.47e+00 pdb=" CG TRP A 627 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 627 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 627 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 627 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 627 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 627 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 627 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 627 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 627 " 0.001 2.00e-02 2.50e+03 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2242 2.77 - 3.30: 11668 3.30 - 3.83: 20685 3.83 - 4.37: 25709 4.37 - 4.90: 45474 Nonbonded interactions: 105778 Sorted by model distance: nonbonded pdb=" OG SER C 437 " pdb=" OD1 ASP C 439 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASN B 229 " pdb=" OG1 THR B 265 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP A 136 " pdb=" NZ LYS A 139 " model vdw 2.320 3.120 nonbonded pdb=" OH TYR C 405 " pdb=" O SER C 538 " model vdw 2.340 3.040 nonbonded pdb=" O CYS B 301 " pdb=" NH1 ARG B 358 " model vdw 2.343 3.120 ... (remaining 105773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 804) selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' } 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: 6.290 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.004 0.051 14262 Z= 0.179 Angle : 0.626 17.953 19442 Z= 0.320 Chirality : 0.048 0.496 2123 Planarity : 0.004 0.078 2428 Dihedral : 12.740 109.322 5515 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1651 helix: -0.50 (0.33), residues: 220 sheet: 0.54 (0.23), residues: 511 loop : -1.23 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 125 TYR 0.011 0.001 TYR B 68 PHE 0.011 0.001 PHE C 537 TRP 0.039 0.002 TRP A 627 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00374 (14222) covalent geometry : angle 0.57875 (19336) SS BOND : bond 0.00522 ( 14) SS BOND : angle 2.33402 ( 28) hydrogen bonds : bond 0.26806 ( 433) hydrogen bonds : angle 7.51536 ( 1212) link_ALPHA1-2 : bond 0.00301 ( 1) link_ALPHA1-2 : angle 1.66488 ( 3) link_ALPHA1-3 : bond 0.00710 ( 1) link_ALPHA1-3 : angle 1.27250 ( 3) link_BETA1-4 : bond 0.00629 ( 7) link_BETA1-4 : angle 1.31191 ( 21) link_BETA1-6 : bond 0.00279 ( 1) link_BETA1-6 : angle 1.44759 ( 3) link_NAG-ASN : bond 0.00365 ( 16) link_NAG-ASN : angle 4.43815 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.8841 (tpt) cc_final: 0.8501 (tpt) REVERT: C 571 MET cc_start: 0.8384 (tpp) cc_final: 0.8165 (tpt) REVERT: C 579 PHE cc_start: 0.8688 (m-80) cc_final: 0.8456 (m-80) outliers start: 2 outliers final: 1 residues processed: 154 average time/residue: 0.8201 time to fit residues: 134.7291 Evaluate side-chains 82 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 473 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.045723 restraints weight = 36187.142| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 3.38 r_work: 0.2446 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14262 Z= 0.125 Angle : 0.597 12.182 19442 Z= 0.306 Chirality : 0.046 0.389 2123 Planarity : 0.004 0.053 2428 Dihedral : 8.645 84.439 2386 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.61 % Allowed : 6.90 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1651 helix: 0.36 (0.33), residues: 242 sheet: 0.81 (0.23), residues: 524 loop : -1.27 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 54 TYR 0.013 0.001 TYR C 456 PHE 0.026 0.001 PHE B 98 TRP 0.009 0.001 TRP B 627 HIS 0.004 0.001 HIS B 750 Details of bonding type rmsd covalent geometry : bond 0.00286 (14222) covalent geometry : angle 0.57193 (19336) SS BOND : bond 0.00272 ( 14) SS BOND : angle 1.28520 ( 28) hydrogen bonds : bond 0.04462 ( 433) hydrogen bonds : angle 5.23959 ( 1212) link_ALPHA1-2 : bond 0.00351 ( 1) link_ALPHA1-2 : angle 1.91677 ( 3) link_ALPHA1-3 : bond 0.01292 ( 1) link_ALPHA1-3 : angle 2.11580 ( 3) link_BETA1-4 : bond 0.00641 ( 7) link_BETA1-4 : angle 2.05241 ( 21) link_BETA1-6 : bond 0.00319 ( 1) link_BETA1-6 : angle 1.34384 ( 3) link_NAG-ASN : bond 0.00445 ( 16) link_NAG-ASN : angle 3.02138 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9040 (t0) cc_final: 0.8498 (t70) REVERT: B 190 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: C 512 ARG cc_start: 0.8625 (tmm-80) cc_final: 0.8165 (tmt90) REVERT: C 530 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8735 (mp0) REVERT: C 575 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7643 (tm) outliers start: 9 outliers final: 3 residues processed: 89 average time/residue: 0.7300 time to fit residues: 70.3154 Evaluate side-chains 81 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 585 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 24 optimal weight: 0.0980 chunk 120 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 130 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 517 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.042992 restraints weight = 36739.543| |-----------------------------------------------------------------------------| r_work (start): 0.2511 rms_B_bonded: 3.39 r_work: 0.2368 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14262 Z= 0.207 Angle : 0.591 11.515 19442 Z= 0.306 Chirality : 0.047 0.426 2123 Planarity : 0.004 0.048 2428 Dihedral : 7.449 72.586 2385 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.01 % Allowed : 8.11 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1651 helix: 0.85 (0.34), residues: 244 sheet: 0.78 (0.23), residues: 522 loop : -1.23 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.017 0.001 TYR A 256 PHE 0.009 0.001 PHE B 89 TRP 0.014 0.001 TRP B 629 HIS 0.006 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00493 (14222) covalent geometry : angle 0.56438 (19336) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.08854 ( 28) hydrogen bonds : bond 0.05252 ( 433) hydrogen bonds : angle 4.96240 ( 1212) link_ALPHA1-2 : bond 0.00392 ( 1) link_ALPHA1-2 : angle 1.97952 ( 3) link_ALPHA1-3 : bond 0.01308 ( 1) link_ALPHA1-3 : angle 1.15601 ( 3) link_BETA1-4 : bond 0.00628 ( 7) link_BETA1-4 : angle 1.88625 ( 21) link_BETA1-6 : bond 0.00213 ( 1) link_BETA1-6 : angle 1.38264 ( 3) link_NAG-ASN : bond 0.00345 ( 16) link_NAG-ASN : angle 3.26638 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9183 (t0) cc_final: 0.8807 (t0) REVERT: B 191 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 461 ARG cc_start: 0.9282 (ptm-80) cc_final: 0.8630 (tpt170) REVERT: C 512 ARG cc_start: 0.8640 (tmm-80) cc_final: 0.8157 (tmt90) REVERT: C 530 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8742 (mp0) REVERT: C 550 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8431 (ttp-110) REVERT: C 575 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7686 (tm) outliers start: 15 outliers final: 5 residues processed: 89 average time/residue: 0.6767 time to fit residues: 65.2064 Evaluate side-chains 80 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.066755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.043904 restraints weight = 36555.808| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 3.30 r_work: 0.2391 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14262 Z= 0.129 Angle : 0.543 13.688 19442 Z= 0.276 Chirality : 0.045 0.432 2123 Planarity : 0.003 0.049 2428 Dihedral : 6.614 63.504 2385 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.81 % Allowed : 8.99 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.20), residues: 1651 helix: 1.03 (0.35), residues: 244 sheet: 0.82 (0.23), residues: 522 loop : -1.18 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 550 TYR 0.011 0.001 TYR B 241 PHE 0.021 0.001 PHE C 431 TRP 0.011 0.001 TRP B 157 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00303 (14222) covalent geometry : angle 0.51670 (19336) SS BOND : bond 0.00172 ( 14) SS BOND : angle 0.79125 ( 28) hydrogen bonds : bond 0.03812 ( 433) hydrogen bonds : angle 4.70091 ( 1212) link_ALPHA1-2 : bond 0.00555 ( 1) link_ALPHA1-2 : angle 1.84744 ( 3) link_ALPHA1-3 : bond 0.01460 ( 1) link_ALPHA1-3 : angle 1.30317 ( 3) link_BETA1-4 : bond 0.00618 ( 7) link_BETA1-4 : angle 1.82695 ( 21) link_BETA1-6 : bond 0.00309 ( 1) link_BETA1-6 : angle 1.26145 ( 3) link_NAG-ASN : bond 0.00377 ( 16) link_NAG-ASN : angle 3.10811 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9187 (t0) cc_final: 0.8795 (t0) REVERT: A 538 LYS cc_start: 0.8680 (mppt) cc_final: 0.8408 (mppt) REVERT: B 191 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8615 (tm-30) REVERT: B 361 GLU cc_start: 0.9456 (pm20) cc_final: 0.9207 (pm20) REVERT: C 461 ARG cc_start: 0.9287 (ptm-80) cc_final: 0.8945 (tpt170) REVERT: C 465 GLN cc_start: 0.9001 (mm110) cc_final: 0.8667 (mp10) REVERT: C 512 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8122 (tmt90) REVERT: C 530 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8738 (mp0) REVERT: C 575 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7583 (tm) outliers start: 12 outliers final: 3 residues processed: 87 average time/residue: 0.6424 time to fit residues: 60.6449 Evaluate side-chains 79 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 4.9990 chunk 128 optimal weight: 0.0050 chunk 77 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 122 optimal weight: 0.3980 chunk 147 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.066680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.043653 restraints weight = 36594.520| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 3.42 r_work: 0.2385 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14262 Z= 0.138 Angle : 0.543 11.567 19442 Z= 0.277 Chirality : 0.045 0.439 2123 Planarity : 0.003 0.048 2428 Dihedral : 6.142 55.705 2385 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.08 % Allowed : 9.33 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1651 helix: 1.13 (0.35), residues: 244 sheet: 0.84 (0.23), residues: 523 loop : -1.14 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 550 TYR 0.011 0.001 TYR A 256 PHE 0.024 0.001 PHE B 98 TRP 0.010 0.001 TRP B 629 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00328 (14222) covalent geometry : angle 0.51689 (19336) SS BOND : bond 0.00187 ( 14) SS BOND : angle 0.78331 ( 28) hydrogen bonds : bond 0.03866 ( 433) hydrogen bonds : angle 4.64312 ( 1212) link_ALPHA1-2 : bond 0.00495 ( 1) link_ALPHA1-2 : angle 1.86075 ( 3) link_ALPHA1-3 : bond 0.01400 ( 1) link_ALPHA1-3 : angle 1.10847 ( 3) link_BETA1-4 : bond 0.00572 ( 7) link_BETA1-4 : angle 1.80189 ( 21) link_BETA1-6 : bond 0.00275 ( 1) link_BETA1-6 : angle 1.29656 ( 3) link_NAG-ASN : bond 0.00323 ( 16) link_NAG-ASN : angle 3.09106 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9193 (t0) cc_final: 0.8769 (t0) REVERT: A 538 LYS cc_start: 0.8691 (mppt) cc_final: 0.8308 (mppt) REVERT: B 361 GLU cc_start: 0.9485 (pm20) cc_final: 0.9213 (pm20) REVERT: C 461 ARG cc_start: 0.9283 (ptm-80) cc_final: 0.8735 (tpt170) REVERT: C 465 GLN cc_start: 0.9064 (mm110) cc_final: 0.8668 (mm110) REVERT: C 512 ARG cc_start: 0.8690 (tmm-80) cc_final: 0.7956 (ttt90) REVERT: C 575 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7649 (tm) outliers start: 16 outliers final: 5 residues processed: 90 average time/residue: 0.7653 time to fit residues: 74.5636 Evaluate side-chains 82 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 130 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 128 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.043728 restraints weight = 36212.565| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 3.36 r_work: 0.2391 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14262 Z= 0.130 Angle : 0.533 11.628 19442 Z= 0.273 Chirality : 0.045 0.451 2123 Planarity : 0.003 0.048 2428 Dihedral : 5.800 50.856 2385 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.22 % Allowed : 9.40 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1651 helix: 1.19 (0.35), residues: 246 sheet: 0.86 (0.23), residues: 523 loop : -1.13 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 550 TYR 0.011 0.001 TYR A 256 PHE 0.025 0.001 PHE C 431 TRP 0.010 0.001 TRP B 629 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00310 (14222) covalent geometry : angle 0.50722 (19336) SS BOND : bond 0.00163 ( 14) SS BOND : angle 0.75863 ( 28) hydrogen bonds : bond 0.03670 ( 433) hydrogen bonds : angle 4.55359 ( 1212) link_ALPHA1-2 : bond 0.00374 ( 1) link_ALPHA1-2 : angle 1.82290 ( 3) link_ALPHA1-3 : bond 0.01385 ( 1) link_ALPHA1-3 : angle 1.11168 ( 3) link_BETA1-4 : bond 0.00507 ( 7) link_BETA1-4 : angle 1.77583 ( 21) link_BETA1-6 : bond 0.00232 ( 1) link_BETA1-6 : angle 1.27747 ( 3) link_NAG-ASN : bond 0.00326 ( 16) link_NAG-ASN : angle 3.07315 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9201 (t0) cc_final: 0.8792 (t0) REVERT: A 538 LYS cc_start: 0.8722 (mppt) cc_final: 0.8349 (mppt) REVERT: B 191 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8616 (tm-30) REVERT: C 408 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8664 (mmmt) REVERT: C 461 ARG cc_start: 0.9276 (ptm-80) cc_final: 0.8735 (tpt170) REVERT: C 465 GLN cc_start: 0.9080 (mm110) cc_final: 0.8776 (mm110) REVERT: C 512 ARG cc_start: 0.8681 (tmm-80) cc_final: 0.8085 (ttt90) REVERT: C 547 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 575 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7650 (tm) outliers start: 18 outliers final: 7 residues processed: 95 average time/residue: 0.7634 time to fit residues: 78.5061 Evaluate side-chains 82 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.042472 restraints weight = 36695.995| |-----------------------------------------------------------------------------| r_work (start): 0.2495 rms_B_bonded: 3.37 r_work: 0.2352 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14262 Z= 0.204 Angle : 0.585 12.194 19442 Z= 0.300 Chirality : 0.047 0.483 2123 Planarity : 0.004 0.048 2428 Dihedral : 5.746 50.969 2385 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.08 % Allowed : 9.74 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1651 helix: 1.09 (0.35), residues: 248 sheet: 0.78 (0.23), residues: 523 loop : -1.16 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 550 TYR 0.015 0.001 TYR A 256 PHE 0.025 0.001 PHE B 98 TRP 0.013 0.001 TRP B 629 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00491 (14222) covalent geometry : angle 0.55770 (19336) SS BOND : bond 0.00214 ( 14) SS BOND : angle 0.89395 ( 28) hydrogen bonds : bond 0.04387 ( 433) hydrogen bonds : angle 4.65806 ( 1212) link_ALPHA1-2 : bond 0.00282 ( 1) link_ALPHA1-2 : angle 1.96173 ( 3) link_ALPHA1-3 : bond 0.01297 ( 1) link_ALPHA1-3 : angle 1.08130 ( 3) link_BETA1-4 : bond 0.00529 ( 7) link_BETA1-4 : angle 1.82518 ( 21) link_BETA1-6 : bond 0.00185 ( 1) link_BETA1-6 : angle 1.41327 ( 3) link_NAG-ASN : bond 0.00281 ( 16) link_NAG-ASN : angle 3.29938 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9242 (t0) cc_final: 0.8868 (t0) REVERT: A 538 LYS cc_start: 0.8738 (mppt) cc_final: 0.8366 (mppt) REVERT: C 408 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8708 (mmmt) REVERT: C 461 ARG cc_start: 0.9271 (ptm-80) cc_final: 0.8839 (tpt170) REVERT: C 465 GLN cc_start: 0.9057 (mm110) cc_final: 0.8814 (mp10) REVERT: C 512 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.8060 (ttt90) REVERT: C 575 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7663 (tm) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.6899 time to fit residues: 64.3358 Evaluate side-chains 82 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 62 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 0.0040 chunk 110 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 104 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 overall best weight: 1.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.066235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.043327 restraints weight = 36165.678| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 3.44 r_work: 0.2378 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14262 Z= 0.132 Angle : 0.558 12.468 19442 Z= 0.283 Chirality : 0.045 0.480 2123 Planarity : 0.003 0.049 2428 Dihedral : 5.589 50.628 2385 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.88 % Allowed : 10.07 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.20), residues: 1651 helix: 1.11 (0.35), residues: 249 sheet: 0.80 (0.23), residues: 524 loop : -1.11 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 550 TYR 0.011 0.001 TYR A 256 PHE 0.027 0.001 PHE C 431 TRP 0.011 0.001 TRP B 157 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00314 (14222) covalent geometry : angle 0.53108 (19336) SS BOND : bond 0.00157 ( 14) SS BOND : angle 0.75167 ( 28) hydrogen bonds : bond 0.03736 ( 433) hydrogen bonds : angle 4.55243 ( 1212) link_ALPHA1-2 : bond 0.00398 ( 1) link_ALPHA1-2 : angle 1.88059 ( 3) link_ALPHA1-3 : bond 0.01298 ( 1) link_ALPHA1-3 : angle 1.07939 ( 3) link_BETA1-4 : bond 0.00547 ( 7) link_BETA1-4 : angle 1.81391 ( 21) link_BETA1-6 : bond 0.00253 ( 1) link_BETA1-6 : angle 1.30495 ( 3) link_NAG-ASN : bond 0.00338 ( 16) link_NAG-ASN : angle 3.22585 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9235 (t0) cc_final: 0.8852 (t0) REVERT: A 538 LYS cc_start: 0.8760 (mppt) cc_final: 0.8386 (mppt) REVERT: C 461 ARG cc_start: 0.9259 (ptm-80) cc_final: 0.8730 (tpt170) REVERT: C 465 GLN cc_start: 0.9103 (mm110) cc_final: 0.8859 (mm110) REVERT: C 509 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8652 (ptpt) REVERT: C 512 ARG cc_start: 0.8706 (tmm-80) cc_final: 0.7975 (ttt90) REVERT: C 575 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (tm) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.7153 time to fit residues: 65.9598 Evaluate side-chains 81 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3049 r_free = 0.3049 target = 0.064056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.041231 restraints weight = 36989.033| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 3.38 r_work: 0.2312 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 14262 Z= 0.315 Angle : 0.677 13.253 19442 Z= 0.346 Chirality : 0.050 0.536 2123 Planarity : 0.004 0.047 2428 Dihedral : 5.838 54.063 2385 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.81 % Allowed : 10.34 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1651 helix: 0.87 (0.35), residues: 249 sheet: 0.74 (0.23), residues: 498 loop : -1.25 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 550 TYR 0.019 0.002 TYR B 256 PHE 0.025 0.001 PHE B 98 TRP 0.017 0.002 TRP B 629 HIS 0.006 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00760 (14222) covalent geometry : angle 0.64806 (19336) SS BOND : bond 0.00272 ( 14) SS BOND : angle 1.07418 ( 28) hydrogen bonds : bond 0.05486 ( 433) hydrogen bonds : angle 4.88272 ( 1212) link_ALPHA1-2 : bond 0.00029 ( 1) link_ALPHA1-2 : angle 2.18476 ( 3) link_ALPHA1-3 : bond 0.01226 ( 1) link_ALPHA1-3 : angle 1.06869 ( 3) link_BETA1-4 : bond 0.00569 ( 7) link_BETA1-4 : angle 1.94700 ( 21) link_BETA1-6 : bond 0.00020 ( 1) link_BETA1-6 : angle 1.56538 ( 3) link_NAG-ASN : bond 0.00329 ( 16) link_NAG-ASN : angle 3.71014 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9306 (t0) cc_final: 0.8952 (t0) REVERT: A 538 LYS cc_start: 0.8789 (mppt) cc_final: 0.8365 (mppt) REVERT: C 461 ARG cc_start: 0.9267 (ptm-80) cc_final: 0.8811 (tpt170) REVERT: C 465 GLN cc_start: 0.9079 (mm110) cc_final: 0.8858 (mp10) REVERT: C 512 ARG cc_start: 0.8870 (tmm-80) cc_final: 0.7885 (ttt90) REVERT: C 521 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7968 (tp30) REVERT: C 575 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7779 (tm) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.6570 time to fit residues: 58.1193 Evaluate side-chains 79 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 20 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.066096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.043262 restraints weight = 36133.487| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 3.41 r_work: 0.2377 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14262 Z= 0.109 Angle : 0.577 13.059 19442 Z= 0.290 Chirality : 0.045 0.486 2123 Planarity : 0.003 0.051 2428 Dihedral : 5.547 49.832 2385 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.61 % Allowed : 10.62 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1651 helix: 1.12 (0.35), residues: 245 sheet: 0.74 (0.23), residues: 524 loop : -1.17 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 550 TYR 0.011 0.001 TYR A 166 PHE 0.024 0.001 PHE C 431 TRP 0.015 0.001 TRP B 157 HIS 0.003 0.001 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00256 (14222) covalent geometry : angle 0.54963 (19336) SS BOND : bond 0.00129 ( 14) SS BOND : angle 0.72852 ( 28) hydrogen bonds : bond 0.03539 ( 433) hydrogen bonds : angle 4.58206 ( 1212) link_ALPHA1-2 : bond 0.00451 ( 1) link_ALPHA1-2 : angle 1.85965 ( 3) link_ALPHA1-3 : bond 0.01215 ( 1) link_ALPHA1-3 : angle 1.02855 ( 3) link_BETA1-4 : bond 0.00589 ( 7) link_BETA1-4 : angle 1.79673 ( 21) link_BETA1-6 : bond 0.00303 ( 1) link_BETA1-6 : angle 1.30562 ( 3) link_NAG-ASN : bond 0.00419 ( 16) link_NAG-ASN : angle 3.30121 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ASP cc_start: 0.9239 (t0) cc_final: 0.8859 (t0) REVERT: A 538 LYS cc_start: 0.8807 (mppt) cc_final: 0.8433 (mppt) REVERT: C 423 LEU cc_start: 0.9228 (mp) cc_final: 0.8942 (pp) REVERT: C 461 ARG cc_start: 0.9246 (ptm-80) cc_final: 0.8684 (tpt170) REVERT: C 465 GLN cc_start: 0.9120 (mm110) cc_final: 0.8890 (mm110) REVERT: C 512 ARG cc_start: 0.8892 (tmm-80) cc_final: 0.8621 (tmm-80) REVERT: C 521 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7905 (tp30) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.6453 time to fit residues: 57.6170 Evaluate side-chains 79 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 472 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 535 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 90 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3095 r_free = 0.3095 target = 0.066114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.043308 restraints weight = 36275.124| |-----------------------------------------------------------------------------| r_work (start): 0.2515 rms_B_bonded: 3.39 r_work: 0.2378 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14262 Z= 0.121 Angle : 0.572 12.581 19442 Z= 0.286 Chirality : 0.045 0.487 2123 Planarity : 0.003 0.053 2428 Dihedral : 5.361 50.426 2385 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.61 % Allowed : 10.75 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1651 helix: 1.19 (0.35), residues: 247 sheet: 0.78 (0.23), residues: 524 loop : -1.14 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 550 TYR 0.010 0.001 TYR B 241 PHE 0.022 0.001 PHE B 98 TRP 0.011 0.001 TRP B 157 HIS 0.002 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00289 (14222) covalent geometry : angle 0.54607 (19336) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.71748 ( 28) hydrogen bonds : bond 0.03542 ( 433) hydrogen bonds : angle 4.50579 ( 1212) link_ALPHA1-2 : bond 0.00366 ( 1) link_ALPHA1-2 : angle 1.86540 ( 3) link_ALPHA1-3 : bond 0.01078 ( 1) link_ALPHA1-3 : angle 1.07576 ( 3) link_BETA1-4 : bond 0.00515 ( 7) link_BETA1-4 : angle 1.77496 ( 21) link_BETA1-6 : bond 0.00210 ( 1) link_BETA1-6 : angle 1.30502 ( 3) link_NAG-ASN : bond 0.00323 ( 16) link_NAG-ASN : angle 3.19544 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.11 seconds wall clock time: 72 minutes 12.74 seconds (4332.74 seconds total)