Starting phenix.real_space_refine on Thu May 15 22:32:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvr_47216/05_2025/9dvr_47216.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 52 5.16 5 C 8816 2.51 5 N 2242 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5889 Classifications: {'peptide': 719} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 685} Chain: "B" Number of atoms: 5889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5889 Classifications: {'peptide': 719} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 685} Chain: "G" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 901 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 901 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "A" 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.80, per 1000 atoms: 0.57 Number of scatterers: 13692 At special positions: 0 Unit cell: (152.22, 81.7, 123.84, 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 52 16.00 O 2582 8.00 N 2242 7.00 C 8816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 321 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 441 " distance=2.03 Simple disulfide: pdb=" SG CYS A 448 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 643 " - pdb=" SG CYS A 755 " distance=2.04 Simple disulfide: pdb=" SG CYS B 321 " - pdb=" SG CYS B 332 " distance=2.03 Simple disulfide: pdb=" SG CYS B 438 " - pdb=" SG CYS B 441 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 643 " - pdb=" SG CYS B 755 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 213 " distance=2.00 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 49 " " NAG A 802 " - " ASN A 92 " " NAG A 803 " - " ASN A 227 " " NAG A 804 " - " ASN A 314 " " NAG B 801 " - " ASN B 314 " " NAG B 802 " - " ASN B 227 " " NAG B 803 " - " ASN B 92 " " NAG B 804 " - " ASN B 49 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3132 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 28 sheets defined 18.9% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.649A pdb=" N ILE A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.674A pdb=" N MET A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.752A pdb=" N ALA A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.792A pdb=" N GLU A 417 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 418' Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 491 through 498 removed outlier: 3.580A pdb=" N GLU A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.635A pdb=" N LEU A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 removed outlier: 3.831A pdb=" N GLY A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.526A pdb=" N TYR A 655 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR A 656 " --> pdb=" O TRP A 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 652 through 656' Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.863A pdb=" N PHE A 664 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 removed outlier: 3.566A pdb=" N TYR A 677 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 690 removed outlier: 3.759A pdb=" N ALA A 686 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 689 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 Processing helix chain 'A' and resid 738 through 757 removed outlier: 4.178A pdb=" N ASN A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.624A pdb=" N ILE B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.528A pdb=" N MET B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.536A pdb=" N ALA B 387 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.511A pdb=" N TYR B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 491 through 498 removed outlier: 3.760A pdb=" N GLU B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 removed outlier: 3.546A pdb=" N GLY B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 594 through 611 removed outlier: 3.536A pdb=" N GLU B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.688A pdb=" N VAL B 629 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.921A pdb=" N TYR B 656 " --> pdb=" O TRP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.884A pdb=" N PHE B 664 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 666 " --> pdb=" O GLU B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 removed outlier: 3.704A pdb=" N LYS B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 679 " --> pdb=" O GLU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 689 removed outlier: 3.697A pdb=" N ALA B 686 " --> pdb=" O MET B 683 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 687 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 689 " --> pdb=" O ALA B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 720 removed outlier: 4.475A pdb=" N SER B 710 " --> pdb=" O HIS B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 4.141A pdb=" N ASN B 742 " --> pdb=" O GLY B 738 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.581A pdb=" N ASN A 60 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 78 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A 88 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN A 80 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER A 86 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 105 removed outlier: 4.508A pdb=" N TYR A 118 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 127 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.872A pdb=" N TYR A 152 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 300 removed outlier: 6.625A pdb=" N GLN A 307 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 296 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS A 305 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP A 298 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG A 303 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 310 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 315 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 291 through 300 removed outlier: 6.625A pdb=" N GLN A 307 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 296 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS A 305 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP A 298 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ARG A 303 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 310 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 315 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.747A pdb=" N ILE A 388 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 397 through 403 removed outlier: 6.552A pdb=" N ILE A 400 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER A 411 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 402 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 410 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 451 through 455 removed outlier: 3.751A pdb=" N TYR A 462 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 476 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE A 487 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 505 through 513 removed outlier: 4.465A pdb=" N VAL A 572 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N TYR A 534 " --> pdb=" O GLU A 615 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 617 " --> pdb=" O TYR A 534 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP A 623 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N CYS A 643 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 618 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE A 645 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 620 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL A 647 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 622 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR A 694 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N MET A 727 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 696 " --> pdb=" O MET A 727 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N TYR A 729 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS A 698 " --> pdb=" O TYR A 729 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.501A pdb=" N ASN B 60 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.551A pdb=" N TYR B 118 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B 127 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 154 removed outlier: 3.866A pdb=" N TYR B 152 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB8, first strand: chain 'B' and resid 192 through 194 Processing sheet with id=AB9, first strand: chain 'B' and resid 233 through 238 Processing sheet with id=AC1, first strand: chain 'B' and resid 291 through 300 removed outlier: 6.599A pdb=" N GLN B 307 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 296 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS B 305 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TRP B 298 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ARG B 303 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 310 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 315 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 291 through 300 removed outlier: 6.599A pdb=" N GLN B 307 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU B 296 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS B 305 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TRP B 298 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ARG B 303 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 310 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 315 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 403 removed outlier: 6.492A pdb=" N ILE B 400 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER B 411 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 402 " --> pdb=" O PHE B 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 451 through 455 removed outlier: 6.646A pdb=" N LEU B 476 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE B 487 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP B 478 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 485 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 505 through 512 removed outlier: 4.401A pdb=" N VAL B 572 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 10.598A pdb=" N TYR B 534 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 617 " --> pdb=" O TYR B 534 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP B 623 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS B 643 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 618 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ILE B 645 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 620 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL B 647 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY B 622 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 694 " --> pdb=" O GLN B 725 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N MET B 727 " --> pdb=" O TYR B 694 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 696 " --> pdb=" O MET B 727 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N TYR B 729 " --> pdb=" O LEU B 696 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS B 698 " --> pdb=" O TYR B 729 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 120 through 125 removed outlier: 3.653A pdb=" N GLN G 120 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 128 through 129 removed outlier: 6.913A pdb=" N MET G 151 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA G 167 " --> pdb=" O MET G 151 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP G 153 " --> pdb=" O VAL G 165 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 120 through 125 removed outlier: 3.690A pdb=" N GLN H 120 " --> pdb=" O SER H 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 128 through 129 removed outlier: 6.854A pdb=" N MET H 151 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA H 167 " --> pdb=" O MET H 151 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP H 153 " --> pdb=" O VAL H 165 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1275 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: 5.47 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4271 1.34 - 1.46: 3819 1.46 - 1.58: 5910 1.58 - 1.70: 6 1.70 - 1.82: 78 Bond restraints: 14084 Sorted by residual: bond pdb=" C7 NAG A 803 " pdb=" N2 NAG A 803 " ideal model delta sigma weight residual 1.346 1.411 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C7 NAG B 802 " pdb=" N2 NAG B 802 " ideal model delta sigma weight residual 1.346 1.411 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 NAG A 801 " pdb=" C2 NAG A 801 " ideal model delta sigma weight residual 1.532 1.592 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C7 NAG B 803 " pdb=" N2 NAG B 803 " ideal model delta sigma weight residual 1.346 1.405 -0.059 2.00e-02 2.50e+03 8.76e+00 bond pdb=" C7 NAG A 802 " pdb=" N2 NAG A 802 " ideal model delta sigma weight residual 1.346 1.405 -0.059 2.00e-02 2.50e+03 8.75e+00 ... (remaining 14079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 18842 1.77 - 3.54: 229 3.54 - 5.31: 50 5.31 - 7.07: 26 7.07 - 8.84: 3 Bond angle restraints: 19150 Sorted by residual: angle pdb=" N TYR A 625 " pdb=" CA TYR A 625 " pdb=" C TYR A 625 " ideal model delta sigma weight residual 114.62 105.78 8.84 1.14e+00 7.69e-01 6.02e+01 angle pdb=" CA TYR A 625 " pdb=" C TYR A 625 " pdb=" N GLY A 626 " ideal model delta sigma weight residual 119.71 115.13 4.58 1.17e+00 7.31e-01 1.53e+01 angle pdb=" C TRP A 623 " pdb=" N SER A 624 " pdb=" CA SER A 624 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" N GLY B 626 " pdb=" CA GLY B 626 " pdb=" C GLY B 626 " ideal model delta sigma weight residual 113.86 108.87 4.99 1.50e+00 4.44e-01 1.11e+01 angle pdb=" C CYS G 213 " pdb=" CA CYS G 213 " pdb=" CB CYS G 213 " ideal model delta sigma weight residual 109.38 114.69 -5.31 1.80e+00 3.09e-01 8.69e+00 ... (remaining 19145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 7769 16.26 - 32.52: 454 32.52 - 48.78: 86 48.78 - 65.04: 21 65.04 - 81.31: 6 Dihedral angle restraints: 8336 sinusoidal: 3396 harmonic: 4940 Sorted by residual: dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 213 " pdb=" CB CYS G 213 " ideal model delta sinusoidal sigma weight residual 93.00 53.91 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA SER A 624 " pdb=" C SER A 624 " pdb=" N TYR A 625 " pdb=" CA TYR A 625 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA VAL A 312 " pdb=" C VAL A 312 " pdb=" N GLN A 313 " pdb=" CA GLN A 313 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1841 0.081 - 0.163: 174 0.163 - 0.244: 9 0.244 - 0.325: 2 0.325 - 0.407: 6 Chirality restraints: 2032 Sorted by residual: chirality pdb=" C2 NAG A 801 " pdb=" C1 NAG A 801 " pdb=" C3 NAG A 801 " pdb=" N2 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.90 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.89 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C2 NAG B 804 " pdb=" C1 NAG B 804 " pdb=" C3 NAG B 804 " pdb=" N2 NAG B 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.89 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 2029 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 282 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 283 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 283 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 283 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 432 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 433 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 418 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 419 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.018 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 87 2.60 - 3.17: 10672 3.17 - 3.75: 19498 3.75 - 4.32: 28561 4.32 - 4.90: 48105 Nonbonded interactions: 106923 Sorted by model distance: nonbonded pdb=" CG1 VAL A 317 " pdb=" OE2 GLU A 337 " model vdw 2.024 3.460 nonbonded pdb=" OE2 GLU A 512 " pdb=" OG1 THR A 517 " model vdw 2.262 3.040 nonbonded pdb=" O GLY A 543 " pdb=" OG SER A 546 " model vdw 2.274 3.040 nonbonded pdb=" O ALA B 347 " pdb=" NH2 ARG B 663 " model vdw 2.317 3.120 nonbonded pdb=" O MET B 665 " pdb=" ND2 ASN B 673 " model vdw 2.320 3.120 ... (remaining 106918 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.090 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14102 Z= 0.182 Angle : 0.595 15.848 19194 Z= 0.304 Chirality : 0.051 0.407 2032 Planarity : 0.003 0.034 2428 Dihedral : 10.962 81.305 5174 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.89 % Allowed : 6.04 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1674 helix: 1.12 (0.38), residues: 214 sheet: 0.42 (0.23), residues: 502 loop : -1.16 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 557 HIS 0.003 0.001 HIS A 477 PHE 0.014 0.001 PHE G 227 TYR 0.016 0.001 TYR B 113 ARG 0.001 0.000 ARG B 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 1.98981 ( 24) hydrogen bonds : bond 0.13944 ( 451) hydrogen bonds : angle 5.93924 ( 1275) SS BOND : bond 0.01028 ( 10) SS BOND : angle 3.67975 ( 20) covalent geometry : bond 0.00369 (14084) covalent geometry : angle 0.57974 (19150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TYR cc_start: 0.8054 (m-80) cc_final: 0.7833 (m-80) REVERT: A 331 ASP cc_start: 0.6285 (t70) cc_final: 0.5874 (m-30) REVERT: A 679 ASN cc_start: 0.7906 (t0) cc_final: 0.7574 (t0) REVERT: B 189 GLU cc_start: 0.6614 (pp20) cc_final: 0.6296 (pp20) REVERT: B 274 TYR cc_start: 0.8220 (t80) cc_final: 0.7922 (t80) REVERT: B 304 VAL cc_start: 0.7228 (OUTLIER) cc_final: 0.6841 (p) REVERT: B 445 LYS cc_start: 0.7646 (tttt) cc_final: 0.7378 (tttm) REVERT: B 490 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7373 (tm-30) outliers start: 13 outliers final: 5 residues processed: 280 average time/residue: 1.1081 time to fit residues: 342.0467 Evaluate side-chains 234 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 676 HIS A 691 ASN A 754 GLN B 137 ASN B 491 ASN B 679 ASN B 691 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127173 restraints weight = 18538.531| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.83 r_work: 0.3647 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14102 Z= 0.123 Angle : 0.537 8.085 19194 Z= 0.285 Chirality : 0.045 0.314 2032 Planarity : 0.004 0.039 2428 Dihedral : 5.264 56.201 2059 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.40 % Allowed : 11.59 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1674 helix: 0.80 (0.38), residues: 226 sheet: 0.49 (0.23), residues: 522 loop : -1.22 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.004 0.001 HIS A 69 PHE 0.013 0.001 PHE G 227 TYR 0.019 0.001 TYR B 625 ARG 0.005 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 8) link_NAG-ASN : angle 1.92001 ( 24) hydrogen bonds : bond 0.04396 ( 451) hydrogen bonds : angle 4.89531 ( 1275) SS BOND : bond 0.00346 ( 10) SS BOND : angle 1.20511 ( 20) covalent geometry : bond 0.00276 (14084) covalent geometry : angle 0.53139 (19150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8297 (ptt90) cc_final: 0.8049 (ptm160) REVERT: A 274 TYR cc_start: 0.8338 (t80) cc_final: 0.8070 (t80) REVERT: A 679 ASN cc_start: 0.7764 (t0) cc_final: 0.7452 (t160) REVERT: B 189 GLU cc_start: 0.6595 (pp20) cc_final: 0.6269 (pp20) REVERT: B 274 TYR cc_start: 0.8320 (t80) cc_final: 0.8003 (t80) REVERT: B 304 VAL cc_start: 0.7169 (OUTLIER) cc_final: 0.6780 (p) REVERT: B 445 LYS cc_start: 0.7689 (tttt) cc_final: 0.7422 (tttm) REVERT: B 490 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7293 (tm-30) REVERT: B 671 ASP cc_start: 0.6803 (m-30) cc_final: 0.6592 (m-30) REVERT: H 188 SER cc_start: 0.8398 (m) cc_final: 0.7799 (t) outliers start: 35 outliers final: 17 residues processed: 254 average time/residue: 1.1234 time to fit residues: 314.2171 Evaluate side-chains 248 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 496 ASN A 691 ASN A 754 GLN B 137 ASN B 491 ASN B 679 ASN B 691 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125879 restraints weight = 18608.269| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.83 r_work: 0.3628 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14102 Z= 0.150 Angle : 0.556 7.675 19194 Z= 0.296 Chirality : 0.045 0.303 2032 Planarity : 0.004 0.046 2428 Dihedral : 5.382 56.673 2057 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.61 % Allowed : 12.62 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1674 helix: 0.50 (0.36), residues: 232 sheet: 0.57 (0.23), residues: 498 loop : -1.26 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS A 69 PHE 0.013 0.002 PHE G 227 TYR 0.019 0.002 TYR B 113 ARG 0.006 0.000 ARG B 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 2.06114 ( 24) hydrogen bonds : bond 0.04472 ( 451) hydrogen bonds : angle 4.78708 ( 1275) SS BOND : bond 0.00398 ( 10) SS BOND : angle 1.09278 ( 20) covalent geometry : bond 0.00347 (14084) covalent geometry : angle 0.55064 (19150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8263 (ptt90) cc_final: 0.8021 (ptm160) REVERT: A 274 TYR cc_start: 0.8387 (t80) cc_final: 0.8157 (t80) REVERT: A 679 ASN cc_start: 0.7879 (t0) cc_final: 0.7566 (t160) REVERT: B 189 GLU cc_start: 0.6596 (pp20) cc_final: 0.6256 (pp20) REVERT: B 304 VAL cc_start: 0.7207 (t) cc_final: 0.6797 (p) REVERT: B 445 LYS cc_start: 0.7704 (tttt) cc_final: 0.7438 (tttm) REVERT: B 490 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7249 (tm-30) REVERT: H 188 SER cc_start: 0.8388 (m) cc_final: 0.7840 (t) outliers start: 38 outliers final: 23 residues processed: 252 average time/residue: 1.1583 time to fit residues: 320.2849 Evaluate side-chains 253 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 151 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 496 ASN A 754 GLN B 137 ASN B 491 ASN B 691 ASN ** B 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.136130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122749 restraints weight = 18482.994| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.81 r_work: 0.3581 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14102 Z= 0.283 Angle : 0.699 11.234 19194 Z= 0.371 Chirality : 0.051 0.309 2032 Planarity : 0.005 0.059 2428 Dihedral : 5.915 58.735 2056 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.43 % Allowed : 13.79 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1674 helix: -0.09 (0.33), residues: 246 sheet: 0.34 (0.23), residues: 496 loop : -1.59 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 199 HIS 0.005 0.001 HIS A 743 PHE 0.020 0.003 PHE G 146 TYR 0.025 0.003 TYR A 113 ARG 0.005 0.001 ARG B 685 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 8) link_NAG-ASN : angle 2.33254 ( 24) hydrogen bonds : bond 0.06042 ( 451) hydrogen bonds : angle 5.16559 ( 1275) SS BOND : bond 0.00600 ( 10) SS BOND : angle 1.29371 ( 20) covalent geometry : bond 0.00679 (14084) covalent geometry : angle 0.69390 (19150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: A 490 GLU cc_start: 0.7485 (tt0) cc_final: 0.7255 (tt0) REVERT: A 514 ASP cc_start: 0.7390 (t0) cc_final: 0.7169 (t0) REVERT: A 569 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 679 ASN cc_start: 0.7941 (t0) cc_final: 0.7632 (t160) REVERT: B 189 GLU cc_start: 0.6667 (pp20) cc_final: 0.6299 (pp20) REVERT: B 304 VAL cc_start: 0.7207 (OUTLIER) cc_final: 0.6841 (p) REVERT: B 445 LYS cc_start: 0.7713 (tttt) cc_final: 0.7470 (tttm) REVERT: B 490 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7282 (tm-30) REVERT: H 188 SER cc_start: 0.8457 (m) cc_final: 0.7915 (t) outliers start: 50 outliers final: 26 residues processed: 275 average time/residue: 1.1623 time to fit residues: 351.2662 Evaluate side-chains 275 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN B 99 ASN B 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.138847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125546 restraints weight = 18577.493| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.79 r_work: 0.3624 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14102 Z= 0.132 Angle : 0.557 6.792 19194 Z= 0.298 Chirality : 0.045 0.293 2032 Planarity : 0.004 0.050 2428 Dihedral : 5.538 58.818 2056 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.95 % Allowed : 14.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1674 helix: 0.63 (0.36), residues: 220 sheet: 0.32 (0.22), residues: 510 loop : -1.28 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 122 HIS 0.003 0.001 HIS A 69 PHE 0.015 0.001 PHE H 227 TYR 0.016 0.002 TYR B 589 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 8) link_NAG-ASN : angle 2.13165 ( 24) hydrogen bonds : bond 0.04248 ( 451) hydrogen bonds : angle 4.79595 ( 1275) SS BOND : bond 0.00302 ( 10) SS BOND : angle 0.97595 ( 20) covalent geometry : bond 0.00302 (14084) covalent geometry : angle 0.55193 (19150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7460 (mtp180) REVERT: A 274 TYR cc_start: 0.8360 (t80) cc_final: 0.8110 (t80) REVERT: A 336 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: A 679 ASN cc_start: 0.7910 (t0) cc_final: 0.7599 (t160) REVERT: B 189 GLU cc_start: 0.6666 (pp20) cc_final: 0.6314 (pp20) REVERT: B 274 TYR cc_start: 0.8176 (t80) cc_final: 0.7909 (t80) REVERT: B 304 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6808 (p) REVERT: B 445 LYS cc_start: 0.7694 (tttt) cc_final: 0.7466 (tttm) REVERT: H 188 SER cc_start: 0.8395 (m) cc_final: 0.7842 (t) outliers start: 43 outliers final: 28 residues processed: 254 average time/residue: 1.1676 time to fit residues: 327.4816 Evaluate side-chains 270 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 114 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 496 ASN A 754 GLN B 99 ASN B 691 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.127185 restraints weight = 18694.290| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.82 r_work: 0.3645 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14102 Z= 0.100 Angle : 0.525 6.324 19194 Z= 0.280 Chirality : 0.044 0.281 2032 Planarity : 0.004 0.043 2428 Dihedral : 5.321 59.745 2056 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.95 % Allowed : 14.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1674 helix: 0.79 (0.37), residues: 222 sheet: 0.35 (0.23), residues: 502 loop : -1.07 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 122 HIS 0.002 0.001 HIS A 69 PHE 0.013 0.001 PHE A 57 TYR 0.026 0.001 TYR B 625 ARG 0.004 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 8) link_NAG-ASN : angle 1.98313 ( 24) hydrogen bonds : bond 0.03650 ( 451) hydrogen bonds : angle 4.64254 ( 1275) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.82250 ( 20) covalent geometry : bond 0.00222 (14084) covalent geometry : angle 0.52065 (19150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7455 (mtp180) REVERT: A 274 TYR cc_start: 0.8378 (t80) cc_final: 0.8146 (t80) REVERT: A 296 LEU cc_start: 0.8105 (tp) cc_final: 0.7900 (tt) REVERT: A 490 GLU cc_start: 0.7472 (tt0) cc_final: 0.7241 (tt0) REVERT: A 679 ASN cc_start: 0.7903 (t0) cc_final: 0.7593 (t160) REVERT: B 189 GLU cc_start: 0.6687 (pp20) cc_final: 0.6323 (pp20) REVERT: B 304 VAL cc_start: 0.7182 (OUTLIER) cc_final: 0.6863 (p) REVERT: B 336 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: B 445 LYS cc_start: 0.7661 (tttt) cc_final: 0.7425 (tttm) REVERT: H 188 SER cc_start: 0.8423 (m) cc_final: 0.7886 (t) outliers start: 43 outliers final: 25 residues processed: 251 average time/residue: 1.1472 time to fit residues: 316.1917 Evaluate side-chains 256 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 496 ASN A 754 GLN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125397 restraints weight = 18687.467| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.79 r_work: 0.3622 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14102 Z= 0.158 Angle : 0.585 8.137 19194 Z= 0.309 Chirality : 0.046 0.288 2032 Planarity : 0.004 0.047 2428 Dihedral : 5.480 59.065 2056 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.02 % Allowed : 15.29 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1674 helix: 0.82 (0.37), residues: 220 sheet: 0.32 (0.23), residues: 486 loop : -1.14 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.003 0.001 HIS A 69 PHE 0.013 0.002 PHE A 368 TYR 0.022 0.002 TYR B 625 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 8) link_NAG-ASN : angle 2.05671 ( 24) hydrogen bonds : bond 0.04455 ( 451) hydrogen bonds : angle 4.75112 ( 1275) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.07165 ( 20) covalent geometry : bond 0.00372 (14084) covalent geometry : angle 0.58012 (19150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7460 (mtp180) REVERT: A 274 TYR cc_start: 0.8379 (t80) cc_final: 0.8158 (t80) REVERT: A 296 LEU cc_start: 0.8078 (tp) cc_final: 0.7875 (tt) REVERT: A 336 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: A 394 LYS cc_start: 0.6898 (tppp) cc_final: 0.6664 (tppp) REVERT: A 490 GLU cc_start: 0.7452 (tt0) cc_final: 0.7213 (tt0) REVERT: A 679 ASN cc_start: 0.7932 (t0) cc_final: 0.7624 (t160) REVERT: B 189 GLU cc_start: 0.6696 (pp20) cc_final: 0.6345 (pp20) REVERT: B 304 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6865 (p) REVERT: B 336 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: B 445 LYS cc_start: 0.7684 (tttt) cc_final: 0.7458 (tttm) REVERT: H 188 SER cc_start: 0.8500 (m) cc_final: 0.7968 (t) outliers start: 44 outliers final: 28 residues processed: 263 average time/residue: 1.2055 time to fit residues: 347.3843 Evaluate side-chains 273 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 496 ASN A 754 GLN B 691 ASN ** B 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124417 restraints weight = 18684.829| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.78 r_work: 0.3609 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14102 Z= 0.204 Angle : 0.623 9.441 19194 Z= 0.329 Chirality : 0.048 0.289 2032 Planarity : 0.004 0.052 2428 Dihedral : 5.651 58.615 2056 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.81 % Allowed : 15.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1674 helix: 0.69 (0.36), residues: 220 sheet: 0.29 (0.22), residues: 494 loop : -1.28 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 327 HIS 0.004 0.001 HIS A 69 PHE 0.016 0.002 PHE A 57 TYR 0.023 0.002 TYR B 589 ARG 0.006 0.001 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 8) link_NAG-ASN : angle 2.13546 ( 24) hydrogen bonds : bond 0.04954 ( 451) hydrogen bonds : angle 4.87747 ( 1275) SS BOND : bond 0.00484 ( 10) SS BOND : angle 1.10429 ( 20) covalent geometry : bond 0.00488 (14084) covalent geometry : angle 0.61802 (19150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: A 274 TYR cc_start: 0.8386 (t80) cc_final: 0.8179 (t80) REVERT: A 336 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: A 473 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6654 (mt) REVERT: A 490 GLU cc_start: 0.7464 (tt0) cc_final: 0.7223 (tt0) REVERT: A 679 ASN cc_start: 0.7948 (t0) cc_final: 0.7650 (t160) REVERT: B 189 GLU cc_start: 0.6646 (pp20) cc_final: 0.6287 (pp20) REVERT: B 304 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6855 (p) REVERT: B 336 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: B 445 LYS cc_start: 0.7716 (tttt) cc_final: 0.7497 (tttm) REVERT: H 188 SER cc_start: 0.8494 (m) cc_final: 0.7964 (t) outliers start: 41 outliers final: 27 residues processed: 263 average time/residue: 1.1709 time to fit residues: 338.0853 Evaluate side-chains 273 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 754 GLN B 99 ASN B 449 GLN B 691 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125521 restraints weight = 18492.437| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.78 r_work: 0.3624 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14102 Z= 0.149 Angle : 0.586 7.854 19194 Z= 0.310 Chirality : 0.046 0.276 2032 Planarity : 0.004 0.049 2428 Dihedral : 5.547 57.206 2056 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.61 % Allowed : 16.46 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1674 helix: 0.77 (0.37), residues: 220 sheet: 0.26 (0.22), residues: 510 loop : -1.26 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 PHE 0.016 0.002 PHE A 57 TYR 0.020 0.002 TYR B 625 ARG 0.009 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 8) link_NAG-ASN : angle 2.03901 ( 24) hydrogen bonds : bond 0.04352 ( 451) hydrogen bonds : angle 4.79075 ( 1275) SS BOND : bond 0.00387 ( 10) SS BOND : angle 1.00192 ( 20) covalent geometry : bond 0.00349 (14084) covalent geometry : angle 0.58083 (19150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7475 (mtp180) REVERT: A 274 TYR cc_start: 0.8396 (t80) cc_final: 0.8193 (t80) REVERT: A 336 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: A 394 LYS cc_start: 0.6981 (tppp) cc_final: 0.6684 (tppp) REVERT: A 473 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6631 (mt) REVERT: A 490 GLU cc_start: 0.7439 (tt0) cc_final: 0.7190 (tt0) REVERT: A 679 ASN cc_start: 0.7923 (t0) cc_final: 0.7614 (t160) REVERT: B 189 GLU cc_start: 0.6673 (pp20) cc_final: 0.6313 (pp20) REVERT: B 304 VAL cc_start: 0.7154 (OUTLIER) cc_final: 0.6848 (p) REVERT: B 445 LYS cc_start: 0.7694 (tttt) cc_final: 0.7477 (tttm) REVERT: H 188 SER cc_start: 0.8496 (m) cc_final: 0.7999 (t) outliers start: 38 outliers final: 32 residues processed: 254 average time/residue: 1.1249 time to fit residues: 316.1394 Evaluate side-chains 273 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 110 optimal weight: 0.0470 chunk 144 optimal weight: 0.2980 chunk 154 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 GLN A 496 ASN A 754 GLN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126064 restraints weight = 18566.838| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.81 r_work: 0.3631 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14102 Z= 0.124 Angle : 0.561 7.713 19194 Z= 0.298 Chirality : 0.045 0.269 2032 Planarity : 0.004 0.047 2428 Dihedral : 5.448 56.768 2056 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.26 % Allowed : 16.94 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1674 helix: 0.85 (0.37), residues: 220 sheet: 0.31 (0.22), residues: 510 loop : -1.20 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 PHE 0.018 0.001 PHE H 227 TYR 0.020 0.001 TYR B 625 ARG 0.006 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 1.97909 ( 24) hydrogen bonds : bond 0.04023 ( 451) hydrogen bonds : angle 4.72597 ( 1275) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.92027 ( 20) covalent geometry : bond 0.00284 (14084) covalent geometry : angle 0.55616 (19150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: A 274 TYR cc_start: 0.8412 (t80) cc_final: 0.8211 (t80) REVERT: A 296 LEU cc_start: 0.8119 (tp) cc_final: 0.7886 (tt) REVERT: A 336 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: A 394 LYS cc_start: 0.6966 (tppp) cc_final: 0.6680 (tppp) REVERT: A 490 GLU cc_start: 0.7423 (tt0) cc_final: 0.7211 (tt0) REVERT: A 679 ASN cc_start: 0.7924 (t0) cc_final: 0.7621 (t160) REVERT: B 189 GLU cc_start: 0.6684 (pp20) cc_final: 0.6316 (pp20) REVERT: B 274 TYR cc_start: 0.8165 (t80) cc_final: 0.7953 (t80) REVERT: B 304 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6849 (p) REVERT: B 445 LYS cc_start: 0.7697 (tttt) cc_final: 0.7467 (tttm) REVERT: H 188 SER cc_start: 0.8501 (m) cc_final: 0.7990 (t) outliers start: 33 outliers final: 28 residues processed: 255 average time/residue: 1.1248 time to fit residues: 315.6382 Evaluate side-chains 268 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 510 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 621 TRP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 496 ASN A 754 GLN B 449 GLN B 691 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125840 restraints weight = 18685.018| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.78 r_work: 0.3629 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14102 Z= 0.141 Angle : 0.572 7.919 19194 Z= 0.304 Chirality : 0.045 0.267 2032 Planarity : 0.004 0.048 2428 Dihedral : 5.450 56.863 2056 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.33 % Allowed : 16.67 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1674 helix: 0.83 (0.37), residues: 220 sheet: 0.33 (0.22), residues: 504 loop : -1.19 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 327 HIS 0.003 0.001 HIS B 69 PHE 0.018 0.002 PHE H 227 TYR 0.020 0.002 TYR B 625 ARG 0.007 0.000 ARG B 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 8) link_NAG-ASN : angle 1.96719 ( 24) hydrogen bonds : bond 0.04197 ( 451) hydrogen bonds : angle 4.72536 ( 1275) SS BOND : bond 0.00368 ( 10) SS BOND : angle 0.95583 ( 20) covalent geometry : bond 0.00329 (14084) covalent geometry : angle 0.56805 (19150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9629.68 seconds wall clock time: 166 minutes 21.33 seconds (9981.33 seconds total)