Starting phenix.real_space_refine on Thu Feb 5 00:18:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2l_64732/02_2026/9v2l_64732.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.114 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 8738 2.51 5 N 2225 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13652 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1586 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 13, 'TRANS': 193} 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: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5942 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 26, 'TRANS': 698} 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: "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 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 13652 At special positions: 0 Unit cell: (92.2236, 129.552, 141.629, 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 2623 8.00 N 2225 7.00 C 8738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 411 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 482 " distance=2.04 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 530 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 447 " distance=2.02 Simple disulfide: pdb=" SG CYS B 454 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 339 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.04 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 454 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 762 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 801 " - " ASN B 85 " " NAG B 802 " - " ASN B 150 " " NAG B 803 " - " ASN B 321 " " NAG B 804 " - " ASN B 92 " " NAG C 801 " - " ASN C 150 " " NAG C 802 " - " ASN C 229 " " NAG C 803 " - " ASN C 685 " " NAG D 1 " - " ASN B 219 " " NAG E 1 " - " ASN B 229 " " NAG F 1 " - " ASN B 281 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 486.0 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: 3122 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 29 sheets defined 20.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.045A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 removed outlier: 4.958A pdb=" N SER A 458 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.927A pdb=" N HIS A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 4.090A pdb=" N ASN A 532 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 533 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 274 through 276 No H-bonds generated for 'chain 'B' and resid 274 through 276' Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.660A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 3.531A pdb=" N MET B 425 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 497 through 505 Processing helix chain 'B' and resid 562 through 571 Processing helix chain 'B' and resid 590 through 595 removed outlier: 3.560A pdb=" N ALA B 593 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B 594 " --> pdb=" O MET B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 616 removed outlier: 3.801A 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 663 through 672 removed outlier: 3.521A pdb=" N ARG B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 670 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 688 through 698 removed outlier: 5.545A pdb=" N GLU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 697 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 725 removed outlier: 4.386A pdb=" N SER B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 763 removed outlier: 3.703A pdb=" N TYR B 752 " --> pdb=" O HIS B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.080A pdb=" N ILE C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 497 through 504 removed outlier: 3.541A pdb=" N ASP C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 571 Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 600 through 615 Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 663 through 671 removed outlier: 3.880A pdb=" N TYR C 670 " --> pdb=" O TYR C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 686 removed outlier: 3.597A pdb=" N SER C 686 " --> pdb=" O HIS C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.785A pdb=" N ALA C 692 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C 695 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C 696 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 697 " --> pdb=" O ASN C 694 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 698 " --> pdb=" O PHE C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 727 removed outlier: 3.838A pdb=" N ILE C 719 " --> pdb=" O GLN C 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 726 " --> pdb=" O ALA C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 764 removed outlier: 3.669A pdb=" N TYR C 752 " --> pdb=" O HIS C 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 413 removed outlier: 3.735A pdb=" N TYR A 413 " --> pdb=" O CYS A 589 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 427 removed outlier: 3.805A pdb=" N MET A 423 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE A 485 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 571 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 444 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.522A pdb=" N TYR A 500 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 561 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS A 506 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 559 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A 508 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 557 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 562 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 543 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.522A pdb=" N TYR A 500 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 561 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS A 506 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 559 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG A 508 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 557 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 7.275A pdb=" N LYS B 41 " --> pdb=" O GLN B 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.799A pdb=" N ILE B 76 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 107 removed outlier: 3.769A pdb=" N ASP B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR B 120 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 129 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 157 removed outlier: 3.670A pdb=" N TRP B 154 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196 removed outlier: 4.266A pdb=" N PHE B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 235 through 240 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.217A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 298 through 307 removed outlier: 5.217A pdb=" N LEU B 300 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR B 322 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB6, first strand: chain 'B' and resid 404 through 410 removed outlier: 6.594A pdb=" N ILE B 418 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE B 407 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR B 416 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA B 409 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 414 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 457 through 461 removed outlier: 6.822A pdb=" N LEU B 482 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 493 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER B 484 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU B 491 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 513 through 519 removed outlier: 3.771A pdb=" N VAL B 575 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 578 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR B 540 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS B 622 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU B 542 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE B 624 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 544 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE B 626 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL B 546 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY B 628 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 649 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 624 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ILE B 651 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 626 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL B 653 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY B 628 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B 700 " --> pdb=" O GLN B 731 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N MET B 733 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 702 " --> pdb=" O MET B 733 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N TYR B 735 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS B 704 " --> pdb=" O TYR B 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.097A pdb=" N LYS C 41 " --> pdb=" O GLN C 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.711A pdb=" N ILE C 76 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 105 through 107 removed outlier: 4.193A pdb=" N TYR C 120 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR C 129 " --> pdb=" O TYR C 120 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE C 134 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 152 through 157 removed outlier: 6.490A pdb=" N VAL C 167 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C 155 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 165 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AC6, first strand: chain 'C' and resid 235 through 240 Processing sheet with id=AC7, first strand: chain 'C' and resid 298 through 302 removed outlier: 6.639A pdb=" N GLN C 314 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 322 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AC9, first strand: chain 'C' and resid 404 through 410 removed outlier: 5.811A pdb=" N ILE C 407 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 418 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 457 through 461 removed outlier: 7.056A pdb=" N TYR C 480 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL C 493 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 482 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 489 " --> pdb=" O SER C 484 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 513 through 519 removed outlier: 3.504A pdb=" N THR C 522 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 575 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE C 578 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR C 540 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LYS C 622 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU C 542 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE C 624 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU C 544 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE C 626 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS C 649 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 624 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N ILE C 651 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE C 626 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL C 653 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLY C 628 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY C 650 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE C 703 " --> pdb=" O GLY C 650 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA C 652 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N GLY C 705 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR C 700 " --> pdb=" O GLN C 731 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N MET C 733 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 702 " --> pdb=" O MET C 733 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR C 735 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS C 704 " --> pdb=" O TYR C 735 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1134 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: 2.93 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2454 1.33 - 1.45: 4075 1.45 - 1.57: 7403 1.57 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 14032 Sorted by residual: bond pdb=" C1 NAG C 803 " pdb=" O5 NAG C 803 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA SER A 514 " pdb=" CB SER A 514 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.51e-02 4.39e+03 1.85e+01 bond pdb=" N THR A 546 " pdb=" CA THR A 546 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 1.453 1.490 -0.036 1.22e-02 6.72e+03 8.94e+00 bond pdb=" N ARG A 547 " pdb=" CA ARG A 547 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.23e-02 6.61e+03 8.69e+00 ... (remaining 14027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 18353 1.80 - 3.59: 622 3.59 - 5.39: 86 5.39 - 7.19: 15 7.19 - 8.99: 6 Bond angle restraints: 19082 Sorted by residual: angle pdb=" N GLY B 632 " pdb=" CA GLY B 632 " pdb=" C GLY B 632 " ideal model delta sigma weight residual 114.66 105.76 8.90 1.24e+00 6.50e-01 5.15e+01 angle pdb=" N TYR B 631 " pdb=" CA TYR B 631 " pdb=" C TYR B 631 " ideal model delta sigma weight residual 114.56 105.57 8.99 1.27e+00 6.20e-01 5.01e+01 angle pdb=" N SER B 242 " pdb=" CA SER B 242 " pdb=" CB SER B 242 " ideal model delta sigma weight residual 114.17 107.27 6.90 1.14e+00 7.69e-01 3.67e+01 angle pdb=" CA GLY A 511 " pdb=" C GLY A 511 " pdb=" O GLY A 511 " ideal model delta sigma weight residual 122.39 118.14 4.25 9.30e-01 1.16e+00 2.09e+01 angle pdb=" N SER B 86 " pdb=" CA SER B 86 " pdb=" C SER B 86 " ideal model delta sigma weight residual 110.91 116.25 -5.34 1.17e+00 7.31e-01 2.09e+01 ... (remaining 19077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.90: 7859 22.90 - 45.80: 456 45.80 - 68.70: 53 68.70 - 91.60: 15 91.60 - 114.49: 18 Dihedral angle restraints: 8401 sinusoidal: 3501 harmonic: 4900 Sorted by residual: dihedral pdb=" CB CYS C 385 " pdb=" SG CYS C 385 " pdb=" SG CYS C 394 " pdb=" CB CYS C 394 " ideal model delta sinusoidal sigma weight residual -86.00 0.21 -86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CA LYS C 139 " pdb=" C LYS C 139 " pdb=" N ARG C 140 " pdb=" CA ARG C 140 " ideal model delta harmonic sigma weight residual 180.00 145.11 34.89 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CB CYS A 429 " pdb=" SG CYS A 429 " pdb=" SG CYS A 482 " pdb=" CB CYS A 482 " ideal model delta sinusoidal sigma weight residual 93.00 35.76 57.24 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 8398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1966 0.106 - 0.213: 92 0.213 - 0.319: 4 0.319 - 0.425: 0 0.425 - 0.532: 1 Chirality restraints: 2063 Sorted by residual: chirality pdb=" C1 NAG C 803 " pdb=" ND2 ASN C 685 " pdb=" C2 NAG C 803 " pdb=" O5 NAG C 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CA GLN A 540 " pdb=" N GLN A 540 " pdb=" C GLN A 540 " pdb=" CB GLN A 540 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C1 NAG B 804 " pdb=" ND2 ASN B 92 " pdb=" C2 NAG B 804 " pdb=" O5 NAG B 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2060 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 630 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C SER B 630 " -0.065 2.00e-02 2.50e+03 pdb=" O SER B 630 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR B 631 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 92 " 0.003 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN B 92 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 92 " -0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN B 92 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG B 804 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 219 " 0.024 2.00e-02 2.50e+03 2.34e-02 6.85e+00 pdb=" CG ASN B 219 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 219 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 219 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.022 2.00e-02 2.50e+03 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 191 2.65 - 3.21: 12017 3.21 - 3.77: 20183 3.77 - 4.34: 31068 4.34 - 4.90: 50709 Nonbonded interactions: 114168 Sorted by model distance: nonbonded pdb=" OD2 ASP C 331 " pdb=" ND2 ASN C 338 " model vdw 2.087 3.120 nonbonded pdb=" O TYR C 43 " pdb=" OG1 THR C 570 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR A 500 " pdb=" OE1 GLN A 572 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 87 " pdb=" O7 NAG B 801 " model vdw 2.219 3.040 nonbonded pdb=" O PHE A 403 " pdb=" OH TYR A 527 " model vdw 2.232 3.040 ... (remaining 114163 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 'B' and resid 40 through 803) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.000 Find NCS groups from input model: 0.200 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:9.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 14059 Z= 0.260 Angle : 0.808 11.338 19149 Z= 0.475 Chirality : 0.051 0.532 2063 Planarity : 0.004 0.047 2416 Dihedral : 15.063 114.494 5237 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.27 % Allowed : 0.34 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1651 helix: -1.59 (0.32), residues: 226 sheet: -0.88 (0.22), residues: 538 loop : -1.84 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 508 TYR 0.041 0.002 TYR A 544 PHE 0.021 0.002 PHE C 396 TRP 0.041 0.002 TRP B 629 HIS 0.012 0.001 HIS B 704 Details of bonding type rmsd covalent geometry : bond 0.00511 (14032) covalent geometry : angle 0.77709 (19082) SS BOND : bond 0.00585 ( 14) SS BOND : angle 2.77033 ( 28) hydrogen bonds : bond 0.22950 ( 402) hydrogen bonds : angle 9.76860 ( 1134) link_BETA1-4 : bond 0.00728 ( 3) link_BETA1-4 : angle 2.08651 ( 9) link_NAG-ASN : bond 0.00592 ( 10) link_NAG-ASN : angle 4.89189 ( 30) *********************** 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 235 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8114 (mtt) cc_final: 0.7806 (mtp) REVERT: B 471 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7444 (mtm180) REVERT: B 670 TYR cc_start: 0.7822 (m-80) cc_final: 0.7537 (m-80) REVERT: C 285 ILE cc_start: 0.8479 (mm) cc_final: 0.8189 (mm) REVERT: C 302 ASP cc_start: 0.7938 (m-30) cc_final: 0.7662 (m-30) REVERT: C 392 LYS cc_start: 0.7905 (mmtp) cc_final: 0.7185 (mmmt) outliers start: 4 outliers final: 1 residues processed: 233 average time/residue: 0.4911 time to fit residues: 127.0723 Evaluate side-chains 184 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 227 GLN ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.103965 restraints weight = 15167.619| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.59 r_work: 0.3017 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14059 Z= 0.129 Angle : 0.668 10.575 19149 Z= 0.339 Chirality : 0.047 0.280 2063 Planarity : 0.004 0.057 2416 Dihedral : 10.170 99.543 2117 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 1.01 % Allowed : 9.24 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.19), residues: 1651 helix: -0.89 (0.32), residues: 228 sheet: -0.61 (0.22), residues: 532 loop : -1.62 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 508 TYR 0.036 0.002 TYR A 452 PHE 0.032 0.002 PHE A 408 TRP 0.012 0.001 TRP B 629 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00287 (14032) covalent geometry : angle 0.65224 (19082) SS BOND : bond 0.00357 ( 14) SS BOND : angle 1.85825 ( 28) hydrogen bonds : bond 0.04486 ( 402) hydrogen bonds : angle 6.57915 ( 1134) link_BETA1-4 : bond 0.00797 ( 3) link_BETA1-4 : angle 2.01275 ( 9) link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 3.18550 ( 30) *********************** 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 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8227 (p90) cc_final: 0.8022 (p90) REVERT: A 452 TYR cc_start: 0.6229 (t80) cc_final: 0.5956 (t80) REVERT: B 273 THR cc_start: 0.8313 (m) cc_final: 0.7970 (p) REVERT: B 452 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: B 471 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8098 (mtm-85) REVERT: B 604 GLU cc_start: 0.7185 (tp30) cc_final: 0.6702 (mp0) REVERT: B 670 TYR cc_start: 0.8210 (m-80) cc_final: 0.7740 (m-80) REVERT: B 726 VAL cc_start: 0.8898 (p) cc_final: 0.8660 (m) REVERT: C 302 ASP cc_start: 0.8219 (m-30) cc_final: 0.7813 (m-30) REVERT: C 392 LYS cc_start: 0.7690 (mmtp) cc_final: 0.6820 (mmmt) outliers start: 15 outliers final: 6 residues processed: 205 average time/residue: 0.4553 time to fit residues: 103.7547 Evaluate side-chains 189 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 212 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN B 66 HIS B 314 GLN C 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.106297 restraints weight = 14814.411| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.87 r_work: 0.3031 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14059 Z= 0.130 Angle : 0.626 10.857 19149 Z= 0.317 Chirality : 0.046 0.299 2063 Planarity : 0.004 0.074 2416 Dihedral : 8.126 97.700 2117 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 1.82 % Allowed : 11.40 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.19), residues: 1651 helix: -0.63 (0.33), residues: 232 sheet: -0.38 (0.22), residues: 528 loop : -1.52 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 508 TYR 0.019 0.001 TYR C 566 PHE 0.031 0.002 PHE A 502 TRP 0.013 0.001 TRP B 216 HIS 0.010 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00299 (14032) covalent geometry : angle 0.61124 (19082) SS BOND : bond 0.00726 ( 14) SS BOND : angle 1.42639 ( 28) hydrogen bonds : bond 0.03828 ( 402) hydrogen bonds : angle 5.96106 ( 1134) link_BETA1-4 : bond 0.00629 ( 3) link_BETA1-4 : angle 1.64042 ( 9) link_NAG-ASN : bond 0.00529 ( 10) link_NAG-ASN : angle 3.15282 ( 30) *********************** 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 228 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8231 (p90) cc_final: 0.8003 (p90) REVERT: B 273 THR cc_start: 0.8273 (m) cc_final: 0.7879 (p) REVERT: B 452 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: B 471 ARG cc_start: 0.8457 (mtm110) cc_final: 0.8018 (mtm180) REVERT: B 518 ILE cc_start: 0.8103 (mp) cc_final: 0.7876 (mm) REVERT: B 544 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8279 (tt) REVERT: B 570 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 604 GLU cc_start: 0.7424 (tp30) cc_final: 0.6865 (mp0) REVERT: B 670 TYR cc_start: 0.8316 (m-80) cc_final: 0.7853 (m-80) REVERT: B 726 VAL cc_start: 0.8798 (p) cc_final: 0.8550 (m) REVERT: C 302 ASP cc_start: 0.8104 (m-30) cc_final: 0.7669 (m-30) REVERT: C 392 LYS cc_start: 0.7585 (mmtp) cc_final: 0.6692 (mmmt) REVERT: C 439 TYR cc_start: 0.8472 (m-10) cc_final: 0.8175 (m-10) outliers start: 27 outliers final: 14 residues processed: 216 average time/residue: 0.4059 time to fit residues: 98.4952 Evaluate side-chains 191 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 731 GLN C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103482 restraints weight = 15059.294| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.80 r_work: 0.3079 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14059 Z= 0.174 Angle : 0.646 11.583 19149 Z= 0.327 Chirality : 0.047 0.322 2063 Planarity : 0.004 0.075 2416 Dihedral : 7.619 95.507 2117 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 2.29 % Allowed : 13.56 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.19), residues: 1651 helix: -0.63 (0.33), residues: 232 sheet: -0.36 (0.22), residues: 523 loop : -1.51 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 317 TYR 0.022 0.002 TYR A 452 PHE 0.036 0.002 PHE A 502 TRP 0.015 0.002 TRP B 216 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00416 (14032) covalent geometry : angle 0.63158 (19082) SS BOND : bond 0.00516 ( 14) SS BOND : angle 1.48237 ( 28) hydrogen bonds : bond 0.03802 ( 402) hydrogen bonds : angle 5.85547 ( 1134) link_BETA1-4 : bond 0.00581 ( 3) link_BETA1-4 : angle 1.65013 ( 9) link_NAG-ASN : bond 0.00459 ( 10) link_NAG-ASN : angle 3.18031 ( 30) *********************** 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 221 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6490 (ptm) REVERT: B 82 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6615 (mt-10) REVERT: B 452 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: B 471 ARG cc_start: 0.8508 (mtm110) cc_final: 0.7911 (mtm180) REVERT: B 518 ILE cc_start: 0.8124 (mp) cc_final: 0.7893 (mm) REVERT: B 544 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8260 (tt) REVERT: B 570 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 604 GLU cc_start: 0.7401 (tp30) cc_final: 0.6839 (mp0) REVERT: B 670 TYR cc_start: 0.8419 (m-80) cc_final: 0.7849 (m-80) REVERT: B 726 VAL cc_start: 0.8770 (p) cc_final: 0.8502 (m) REVERT: C 146 GLU cc_start: 0.8312 (mp0) cc_final: 0.8104 (mp0) REVERT: C 392 LYS cc_start: 0.7580 (mmtp) cc_final: 0.6679 (mmpt) REVERT: C 673 LEU cc_start: 0.8530 (mp) cc_final: 0.8327 (mm) outliers start: 34 outliers final: 15 residues processed: 210 average time/residue: 0.4411 time to fit residues: 103.3632 Evaluate side-chains 197 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 140 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 383 HIS C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.103608 restraints weight = 15102.593| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.00 r_work: 0.3011 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14059 Z= 0.188 Angle : 0.661 10.094 19149 Z= 0.336 Chirality : 0.047 0.329 2063 Planarity : 0.004 0.064 2416 Dihedral : 8.248 98.902 2117 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.67 % Rotamer: Outliers : 2.36 % Allowed : 14.84 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1651 helix: -0.79 (0.33), residues: 244 sheet: -0.36 (0.22), residues: 523 loop : -1.55 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 336 TYR 0.015 0.002 TYR C 735 PHE 0.038 0.002 PHE A 502 TRP 0.016 0.002 TRP B 216 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00456 (14032) covalent geometry : angle 0.64511 (19082) SS BOND : bond 0.00501 ( 14) SS BOND : angle 1.71196 ( 28) hydrogen bonds : bond 0.03796 ( 402) hydrogen bonds : angle 5.80333 ( 1134) link_BETA1-4 : bond 0.00625 ( 3) link_BETA1-4 : angle 1.69917 ( 9) link_NAG-ASN : bond 0.00472 ( 10) link_NAG-ASN : angle 3.30605 ( 30) *********************** 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 219 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 GLN cc_start: 0.7987 (tt0) cc_final: 0.7775 (mm-40) REVERT: B 82 GLU cc_start: 0.7702 (mm-30) cc_final: 0.6653 (mt-10) REVERT: B 452 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: B 471 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8130 (mtm180) REVERT: B 518 ILE cc_start: 0.8150 (mp) cc_final: 0.7900 (mm) REVERT: B 570 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7795 (p) REVERT: B 604 GLU cc_start: 0.7398 (tp30) cc_final: 0.6836 (mp0) REVERT: B 670 TYR cc_start: 0.8485 (m-80) cc_final: 0.8039 (m-80) REVERT: C 53 TYR cc_start: 0.8453 (m-80) cc_final: 0.8202 (m-80) REVERT: C 146 GLU cc_start: 0.8454 (mp0) cc_final: 0.8199 (mp0) REVERT: C 378 GLU cc_start: 0.8107 (pm20) cc_final: 0.7595 (pt0) REVERT: C 392 LYS cc_start: 0.7585 (mmtp) cc_final: 0.6685 (mmpt) REVERT: C 589 LYS cc_start: 0.7547 (ttpp) cc_final: 0.7298 (tptp) outliers start: 35 outliers final: 19 residues processed: 205 average time/residue: 0.4811 time to fit residues: 109.7312 Evaluate side-chains 193 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 736 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 28 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.103900 restraints weight = 15089.950| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.80 r_work: 0.3055 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14059 Z= 0.137 Angle : 0.650 19.967 19149 Z= 0.329 Chirality : 0.047 0.348 2063 Planarity : 0.004 0.066 2416 Dihedral : 7.879 95.062 2116 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 2.56 % Allowed : 15.45 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.20), residues: 1651 helix: -0.38 (0.34), residues: 232 sheet: -0.28 (0.22), residues: 525 loop : -1.50 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.014 0.001 TYR A 473 PHE 0.039 0.001 PHE A 502 TRP 0.012 0.001 TRP B 216 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00321 (14032) covalent geometry : angle 0.62706 (19082) SS BOND : bond 0.00606 ( 14) SS BOND : angle 3.03069 ( 28) hydrogen bonds : bond 0.03458 ( 402) hydrogen bonds : angle 5.63120 ( 1134) link_BETA1-4 : bond 0.00682 ( 3) link_BETA1-4 : angle 1.65288 ( 9) link_NAG-ASN : bond 0.00306 ( 10) link_NAG-ASN : angle 3.24818 ( 30) *********************** 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 225 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 GLU cc_start: 0.7643 (mm-30) cc_final: 0.6610 (mt-10) REVERT: B 452 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: B 471 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7931 (mtm180) REVERT: B 518 ILE cc_start: 0.8176 (mp) cc_final: 0.7963 (mm) REVERT: B 570 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 604 GLU cc_start: 0.7411 (tp30) cc_final: 0.6822 (mp0) REVERT: B 670 TYR cc_start: 0.8466 (m-80) cc_final: 0.8033 (m-80) REVERT: B 738 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 53 TYR cc_start: 0.8431 (m-80) cc_final: 0.8204 (m-80) REVERT: C 146 GLU cc_start: 0.8436 (mp0) cc_final: 0.8180 (mp0) REVERT: C 378 GLU cc_start: 0.8121 (pm20) cc_final: 0.7593 (pt0) REVERT: C 392 LYS cc_start: 0.7491 (mmtp) cc_final: 0.6608 (mmpt) REVERT: C 589 LYS cc_start: 0.7554 (ttpp) cc_final: 0.7312 (tptp) outliers start: 38 outliers final: 22 residues processed: 215 average time/residue: 0.4513 time to fit residues: 108.4627 Evaluate side-chains 203 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 677 GLU Chi-restraints excluded: chain C residue 736 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.0170 chunk 71 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 74 ASN C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.106862 restraints weight = 14905.363| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.04 r_work: 0.3054 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14059 Z= 0.122 Angle : 0.634 16.573 19149 Z= 0.319 Chirality : 0.046 0.322 2063 Planarity : 0.004 0.060 2416 Dihedral : 7.730 91.503 2116 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.09 % Allowed : 16.67 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.20), residues: 1651 helix: -0.21 (0.34), residues: 232 sheet: -0.25 (0.22), residues: 525 loop : -1.48 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.019 0.001 TYR A 452 PHE 0.035 0.001 PHE A 502 TRP 0.012 0.001 TRP B 157 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00283 (14032) covalent geometry : angle 0.60999 (19082) SS BOND : bond 0.00605 ( 14) SS BOND : angle 2.96195 ( 28) hydrogen bonds : bond 0.03323 ( 402) hydrogen bonds : angle 5.46123 ( 1134) link_BETA1-4 : bond 0.00597 ( 3) link_BETA1-4 : angle 1.48486 ( 9) link_NAG-ASN : bond 0.00399 ( 10) link_NAG-ASN : angle 3.35588 ( 30) *********************** 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 222 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6629 (mt-10) REVERT: B 452 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: B 471 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8059 (mtm180) REVERT: B 570 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 604 GLU cc_start: 0.7360 (tp30) cc_final: 0.6810 (mp0) REVERT: B 670 TYR cc_start: 0.8469 (m-80) cc_final: 0.8126 (m-80) REVERT: B 738 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7722 (mm-30) REVERT: C 53 TYR cc_start: 0.8407 (m-80) cc_final: 0.8139 (m-80) REVERT: C 146 GLU cc_start: 0.8457 (mp0) cc_final: 0.8183 (mp0) REVERT: C 589 LYS cc_start: 0.7585 (ttpp) cc_final: 0.7349 (tptp) outliers start: 31 outliers final: 20 residues processed: 212 average time/residue: 0.4895 time to fit residues: 115.4029 Evaluate side-chains 205 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 74 ASN C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107528 restraints weight = 14744.351| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.87 r_work: 0.3095 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14059 Z= 0.121 Angle : 0.633 13.401 19149 Z= 0.318 Chirality : 0.046 0.308 2063 Planarity : 0.004 0.062 2416 Dihedral : 7.516 88.560 2116 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.96 % Allowed : 17.07 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1651 helix: -0.14 (0.34), residues: 234 sheet: -0.23 (0.22), residues: 525 loop : -1.43 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.014 0.001 TYR A 473 PHE 0.037 0.001 PHE A 502 TRP 0.012 0.001 TRP B 216 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00284 (14032) covalent geometry : angle 0.60791 (19082) SS BOND : bond 0.00497 ( 14) SS BOND : angle 3.05225 ( 28) hydrogen bonds : bond 0.03280 ( 402) hydrogen bonds : angle 5.40701 ( 1134) link_BETA1-4 : bond 0.00608 ( 3) link_BETA1-4 : angle 1.43497 ( 9) link_NAG-ASN : bond 0.00303 ( 10) link_NAG-ASN : angle 3.33990 ( 30) *********************** 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 213 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 425 ASN cc_start: 0.8664 (m-40) cc_final: 0.8426 (m110) REVERT: B 82 GLU cc_start: 0.7602 (mm-30) cc_final: 0.6632 (mt-10) REVERT: B 452 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: B 471 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7958 (mtm180) REVERT: B 604 GLU cc_start: 0.7342 (tp30) cc_final: 0.6847 (mp0) REVERT: B 670 TYR cc_start: 0.8477 (m-80) cc_final: 0.8034 (m-80) REVERT: B 738 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 146 GLU cc_start: 0.8460 (mp0) cc_final: 0.8250 (mp0) REVERT: C 378 GLU cc_start: 0.8134 (pm20) cc_final: 0.7666 (pt0) REVERT: C 589 LYS cc_start: 0.7614 (ttpp) cc_final: 0.7396 (tptp) outliers start: 29 outliers final: 22 residues processed: 202 average time/residue: 0.4910 time to fit residues: 110.3647 Evaluate side-chains 202 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 736 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104340 restraints weight = 15043.978| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.99 r_work: 0.3064 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14059 Z= 0.198 Angle : 0.684 12.270 19149 Z= 0.343 Chirality : 0.048 0.330 2063 Planarity : 0.004 0.060 2416 Dihedral : 7.626 88.425 2116 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 1.82 % Allowed : 17.21 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.20), residues: 1651 helix: -0.47 (0.33), residues: 244 sheet: -0.32 (0.22), residues: 525 loop : -1.52 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.016 0.002 TYR B 414 PHE 0.037 0.002 PHE A 502 TRP 0.015 0.002 TRP B 216 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00481 (14032) covalent geometry : angle 0.65882 (19082) SS BOND : bond 0.00608 ( 14) SS BOND : angle 2.73311 ( 28) hydrogen bonds : bond 0.03655 ( 402) hydrogen bonds : angle 5.54887 ( 1134) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 1.49096 ( 9) link_NAG-ASN : bond 0.00480 ( 10) link_NAG-ASN : angle 3.87043 ( 30) *********************** 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 208 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 425 ASN cc_start: 0.8676 (m-40) cc_final: 0.8424 (m110) REVERT: A 445 LEU cc_start: 0.7949 (mt) cc_final: 0.7460 (tm) REVERT: B 82 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6694 (mt-10) REVERT: B 137 LEU cc_start: 0.7771 (mt) cc_final: 0.7439 (mp) REVERT: B 452 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: B 471 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: B 570 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7725 (p) REVERT: B 604 GLU cc_start: 0.7433 (tp30) cc_final: 0.6859 (mp0) REVERT: B 670 TYR cc_start: 0.8543 (m-80) cc_final: 0.8178 (m-80) REVERT: B 693 GLU cc_start: 0.7700 (mp0) cc_final: 0.7167 (mp0) REVERT: B 738 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7778 (mm-30) REVERT: C 146 GLU cc_start: 0.8444 (mp0) cc_final: 0.8239 (mp0) REVERT: C 378 GLU cc_start: 0.8081 (pm20) cc_final: 0.7645 (pt0) REVERT: C 589 LYS cc_start: 0.7620 (ttpp) cc_final: 0.7393 (tptp) outliers start: 27 outliers final: 21 residues processed: 199 average time/residue: 0.4957 time to fit residues: 109.2893 Evaluate side-chains 200 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 612 GLN Chi-restraints excluded: chain C residue 736 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 chunk 156 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 74 ASN C 420 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111060 restraints weight = 14773.438| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.08 r_work: 0.3060 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14059 Z= 0.114 Angle : 0.630 13.240 19149 Z= 0.316 Chirality : 0.045 0.298 2063 Planarity : 0.004 0.059 2416 Dihedral : 7.362 84.272 2116 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.75 % Allowed : 17.34 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.20), residues: 1651 helix: -0.09 (0.34), residues: 234 sheet: -0.21 (0.22), residues: 525 loop : -1.42 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.022 0.001 TYR A 452 PHE 0.037 0.001 PHE A 502 TRP 0.013 0.001 TRP B 157 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00262 (14032) covalent geometry : angle 0.60124 (19082) SS BOND : bond 0.00435 ( 14) SS BOND : angle 3.17849 ( 28) hydrogen bonds : bond 0.03240 ( 402) hydrogen bonds : angle 5.36221 ( 1134) link_BETA1-4 : bond 0.00613 ( 3) link_BETA1-4 : angle 1.46622 ( 9) link_NAG-ASN : bond 0.00384 ( 10) link_NAG-ASN : angle 3.68451 ( 30) ********************** 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 212 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 445 LEU cc_start: 0.7957 (mt) cc_final: 0.7456 (tm) REVERT: B 275 SER cc_start: 0.8027 (t) cc_final: 0.7826 (p) REVERT: B 452 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: B 471 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8105 (mtm180) REVERT: B 604 GLU cc_start: 0.7378 (tp30) cc_final: 0.6871 (mp0) REVERT: B 670 TYR cc_start: 0.8507 (m-80) cc_final: 0.8228 (m-80) REVERT: B 738 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 378 GLU cc_start: 0.8171 (pm20) cc_final: 0.7684 (pt0) REVERT: C 589 LYS cc_start: 0.7640 (ttpp) cc_final: 0.7418 (tptp) REVERT: C 604 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7123 (mt-10) REVERT: C 612 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7531 (mt0) outliers start: 26 outliers final: 18 residues processed: 203 average time/residue: 0.5247 time to fit residues: 117.8871 Evaluate side-chains 193 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 612 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 158 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 74 ASN B 314 GLN B 320 GLN C 420 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111184 restraints weight = 14850.714| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.04 r_work: 0.3055 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 14059 Z= 0.151 Angle : 0.833 59.156 19149 Z= 0.471 Chirality : 0.047 0.519 2063 Planarity : 0.004 0.072 2416 Dihedral : 7.373 84.228 2116 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 1.75 % Allowed : 17.68 % Favored : 80.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.20), residues: 1651 helix: -0.08 (0.34), residues: 234 sheet: -0.20 (0.22), residues: 525 loop : -1.41 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 147 TYR 0.016 0.001 TYR A 473 PHE 0.033 0.001 PHE A 502 TRP 0.012 0.001 TRP B 157 HIS 0.009 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00337 (14032) covalent geometry : angle 0.81218 (19082) SS BOND : bond 0.00468 ( 14) SS BOND : angle 3.11308 ( 28) hydrogen bonds : bond 0.03235 ( 402) hydrogen bonds : angle 5.36172 ( 1134) link_BETA1-4 : bond 0.00613 ( 3) link_BETA1-4 : angle 1.46415 ( 9) link_NAG-ASN : bond 0.00376 ( 10) link_NAG-ASN : angle 3.69312 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4378.18 seconds wall clock time: 75 minutes 33.39 seconds (4533.39 seconds total)