Starting phenix.real_space_refine on Thu Sep 18 03:31:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvr_47216/09_2025/9dvr_47216.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvr_47216/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dvr_47216/09_2025/9dvr_47216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvr_47216/09_2025/9dvr_47216.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvr_47216/09_2025/9dvr_47216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvr_47216/09_2025/9dvr_47216.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.41, per 1000 atoms: 0.25 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: 1.06 Conformation dependent library (CDL) restraints added in 655.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 2.95 Time building geometry restraints manager: 1.46 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: 0.01 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: 2.100 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.570 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 311 TYR 0.016 0.001 TYR B 113 PHE 0.014 0.001 PHE G 227 TRP 0.011 0.001 TRP B 557 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00369 (14084) covalent geometry : angle 0.57974 (19150) SS BOND : bond 0.01028 ( 10) SS BOND : angle 3.67975 ( 20) hydrogen bonds : bond 0.13944 ( 451) hydrogen bonds : angle 5.93924 ( 1275) link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 1.98981 ( 24) *********************** 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 : 0.545 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: 0.5824 time to fit residues: 179.1562 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 : 0.353 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.141023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127516 restraints weight = 18635.454| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.84 r_work: 0.3651 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14102 Z= 0.113 Angle : 0.528 7.995 19194 Z= 0.281 Chirality : 0.045 0.321 2032 Planarity : 0.004 0.037 2428 Dihedral : 5.247 56.247 2059 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.47 % Allowed : 11.66 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.21), residues: 1674 helix: 0.79 (0.38), residues: 226 sheet: 0.49 (0.23), residues: 522 loop : -1.21 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 263 TYR 0.019 0.001 TYR B 625 PHE 0.012 0.001 PHE G 227 TRP 0.008 0.001 TRP B 155 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00251 (14084) covalent geometry : angle 0.52265 (19150) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.11571 ( 20) hydrogen bonds : bond 0.04106 ( 451) hydrogen bonds : angle 4.84702 ( 1275) link_NAG-ASN : bond 0.00376 ( 8) link_NAG-ASN : angle 1.90294 ( 24) *********************** 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: 36 poor density : 240 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8310 (ptt90) cc_final: 0.8059 (ptm160) REVERT: A 274 TYR cc_start: 0.8352 (t80) cc_final: 0.8087 (t80) REVERT: A 679 ASN cc_start: 0.7778 (t0) cc_final: 0.7461 (t160) REVERT: B 95 MET cc_start: 0.8319 (mtp) cc_final: 0.8077 (mmm) REVERT: B 189 GLU cc_start: 0.6605 (pp20) cc_final: 0.6276 (pp20) REVERT: B 274 TYR cc_start: 0.8329 (t80) cc_final: 0.7998 (t80) REVERT: B 304 VAL cc_start: 0.7170 (OUTLIER) cc_final: 0.6776 (p) REVERT: B 445 LYS cc_start: 0.7684 (tttt) cc_final: 0.7415 (tttm) REVERT: B 490 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7289 (tm-30) REVERT: H 188 SER cc_start: 0.8399 (m) cc_final: 0.7801 (t) outliers start: 36 outliers final: 17 residues processed: 255 average time/residue: 0.5836 time to fit residues: 163.6057 Evaluate side-chains 245 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 140 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 0.0470 chunk 151 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 111 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.140479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126955 restraints weight = 18770.697| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.85 r_work: 0.3644 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14102 Z= 0.119 Angle : 0.522 7.430 19194 Z= 0.278 Chirality : 0.044 0.303 2032 Planarity : 0.004 0.039 2428 Dihedral : 5.219 56.132 2057 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.33 % Allowed : 12.76 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1674 helix: 0.68 (0.37), residues: 228 sheet: 0.48 (0.22), residues: 524 loop : -1.18 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 343 TYR 0.017 0.001 TYR B 113 PHE 0.012 0.001 PHE G 227 TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00271 (14084) covalent geometry : angle 0.51690 (19150) SS BOND : bond 0.00303 ( 10) SS BOND : angle 0.99276 ( 20) hydrogen bonds : bond 0.04049 ( 451) hydrogen bonds : angle 4.67567 ( 1275) link_NAG-ASN : bond 0.00450 ( 8) link_NAG-ASN : angle 2.00921 ( 24) *********************** 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 266 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8291 (ptt90) cc_final: 0.8051 (ptm160) REVERT: A 263 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7489 (mtp180) REVERT: A 274 TYR cc_start: 0.8382 (t80) cc_final: 0.8140 (t80) REVERT: A 679 ASN cc_start: 0.7858 (t0) cc_final: 0.7555 (t160) REVERT: B 95 MET cc_start: 0.8322 (mtp) cc_final: 0.8096 (mmm) REVERT: B 189 GLU cc_start: 0.6581 (pp20) cc_final: 0.6265 (pp20) REVERT: B 304 VAL cc_start: 0.7194 (OUTLIER) cc_final: 0.6789 (p) REVERT: B 445 LYS cc_start: 0.7682 (tttt) cc_final: 0.7422 (tttm) REVERT: B 490 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7271 (tm-30) REVERT: H 188 SER cc_start: 0.8391 (m) cc_final: 0.7841 (t) outliers start: 34 outliers final: 18 residues processed: 246 average time/residue: 0.6065 time to fit residues: 163.7538 Evaluate side-chains 247 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 510 LYS 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 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 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 96 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125581 restraints weight = 18525.351| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.83 r_work: 0.3624 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14102 Z= 0.159 Angle : 0.568 7.965 19194 Z= 0.302 Chirality : 0.046 0.295 2032 Planarity : 0.004 0.046 2428 Dihedral : 5.404 56.973 2057 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.81 % Allowed : 13.58 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1674 helix: 0.63 (0.36), residues: 232 sheet: 0.55 (0.23), residues: 498 loop : -1.23 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 343 TYR 0.019 0.002 TYR B 113 PHE 0.012 0.002 PHE A 368 TRP 0.009 0.001 TRP B 155 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00372 (14084) covalent geometry : angle 0.56290 (19150) SS BOND : bond 0.00395 ( 10) SS BOND : angle 1.03234 ( 20) hydrogen bonds : bond 0.04495 ( 451) hydrogen bonds : angle 4.73251 ( 1275) link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 2.03236 ( 24) *********************** 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 280 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 239 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8265 (ptt90) cc_final: 0.8028 (ptm160) REVERT: A 263 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: A 274 TYR cc_start: 0.8405 (t80) cc_final: 0.8186 (t80) REVERT: A 297 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.7374 (t) REVERT: A 679 ASN cc_start: 0.7874 (t0) cc_final: 0.7583 (t160) REVERT: B 189 GLU cc_start: 0.6595 (pp20) cc_final: 0.6245 (pp20) REVERT: B 274 TYR cc_start: 0.8273 (t80) cc_final: 0.7980 (t80) REVERT: B 304 VAL cc_start: 0.7210 (t) cc_final: 0.6796 (p) REVERT: B 445 LYS cc_start: 0.7710 (tttt) cc_final: 0.7447 (tttm) REVERT: B 490 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7259 (tm-30) REVERT: H 188 SER cc_start: 0.8393 (m) cc_final: 0.7832 (t) outliers start: 41 outliers final: 24 residues processed: 256 average time/residue: 0.6040 time to fit residues: 169.6718 Evaluate side-chains 257 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 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 363 SER 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 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 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 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 chunk 147 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 491 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 = 0.3912 r_free = 0.3912 target = 0.140759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127280 restraints weight = 18724.786| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.84 r_work: 0.3647 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14102 Z= 0.108 Angle : 0.517 7.756 19194 Z= 0.276 Chirality : 0.044 0.295 2032 Planarity : 0.003 0.042 2428 Dihedral : 5.233 57.274 2056 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.02 % Allowed : 13.72 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1674 helix: 0.53 (0.36), residues: 238 sheet: 0.42 (0.23), residues: 496 loop : -1.15 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 263 TYR 0.023 0.001 TYR B 625 PHE 0.012 0.001 PHE G 227 TRP 0.009 0.001 TRP A 122 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00243 (14084) covalent geometry : angle 0.51197 (19150) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.86996 ( 20) hydrogen bonds : bond 0.03785 ( 451) hydrogen bonds : angle 4.60303 ( 1275) link_NAG-ASN : bond 0.00441 ( 8) link_NAG-ASN : angle 2.01398 ( 24) *********************** 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 273 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8280 (ptt90) cc_final: 0.8051 (ptm160) REVERT: A 263 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7487 (mtp180) REVERT: A 274 TYR cc_start: 0.8396 (t80) cc_final: 0.8180 (t80) REVERT: A 336 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7608 (mt0) REVERT: A 490 GLU cc_start: 0.7455 (tt0) cc_final: 0.7236 (tt0) REVERT: A 679 ASN cc_start: 0.7904 (t0) cc_final: 0.7591 (t160) REVERT: B 95 MET cc_start: 0.8421 (mmm) cc_final: 0.8212 (mmm) REVERT: B 189 GLU cc_start: 0.6654 (pp20) cc_final: 0.6300 (pp20) REVERT: B 304 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6783 (p) REVERT: B 336 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: B 445 LYS cc_start: 0.7687 (tttt) cc_final: 0.7433 (tttm) REVERT: B 490 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7273 (tm-30) REVERT: H 188 SER cc_start: 0.8393 (m) cc_final: 0.7823 (t) outliers start: 44 outliers final: 25 residues processed: 249 average time/residue: 0.5606 time to fit residues: 153.3795 Evaluate side-chains 255 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 336 GLN 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 112 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 212 LEU 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 336 GLN 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 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 166 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 164 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 754 GLN B 691 ASN B 754 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.140256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126899 restraints weight = 18550.997| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.79 r_work: 0.3647 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1382 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= 0.122 Angle : 0.534 7.814 19194 Z= 0.284 Chirality : 0.044 0.296 2032 Planarity : 0.004 0.041 2428 Dihedral : 5.246 58.279 2056 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.09 % Allowed : 13.37 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1674 helix: 0.42 (0.35), residues: 244 sheet: 0.39 (0.23), residues: 496 loop : -1.13 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.020 0.001 TYR B 625 PHE 0.011 0.001 PHE A 57 TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00281 (14084) covalent geometry : angle 0.52869 (19150) SS BOND : bond 0.00296 ( 10) SS BOND : angle 0.93613 ( 20) hydrogen bonds : bond 0.03912 ( 451) hydrogen bonds : angle 4.61050 ( 1275) link_NAG-ASN : bond 0.00440 ( 8) link_NAG-ASN : angle 2.05684 ( 24) *********************** 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 275 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7470 (mtp180) REVERT: A 274 TYR cc_start: 0.8393 (t80) cc_final: 0.8186 (t80) REVERT: A 336 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: A 394 LYS cc_start: 0.6899 (tppp) cc_final: 0.6688 (tppp) REVERT: A 490 GLU cc_start: 0.7452 (tt0) cc_final: 0.7227 (tt0) REVERT: A 679 ASN cc_start: 0.7878 (t0) cc_final: 0.7577 (t160) REVERT: B 189 GLU cc_start: 0.6644 (pp20) cc_final: 0.6309 (pp20) REVERT: B 274 TYR cc_start: 0.8218 (t80) cc_final: 0.7944 (t80) REVERT: B 304 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6759 (p) REVERT: B 336 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: B 445 LYS cc_start: 0.7690 (tttt) cc_final: 0.7448 (tttm) REVERT: B 490 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7258 (tm-30) REVERT: G 196 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6330 (mt) REVERT: H 188 SER cc_start: 0.8410 (m) cc_final: 0.7849 (t) REVERT: H 212 TYR cc_start: 0.8087 (m-80) cc_final: 0.7848 (m-10) outliers start: 45 outliers final: 27 residues processed: 253 average time/residue: 0.5665 time to fit residues: 157.5207 Evaluate side-chains 257 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 336 GLN 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 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 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 166 SER Chi-restraints excluded: chain G residue 196 LEU 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 196 LEU Chi-restraints excluded: chain H residue 238 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 754 GLN B 691 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.126691 restraints weight = 18658.623| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.80 r_work: 0.3641 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14102 Z= 0.130 Angle : 0.540 8.019 19194 Z= 0.288 Chirality : 0.045 0.292 2032 Planarity : 0.004 0.042 2428 Dihedral : 5.295 59.546 2056 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.88 % Allowed : 14.75 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1674 helix: 0.66 (0.36), residues: 232 sheet: 0.30 (0.23), residues: 500 loop : -1.06 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.018 0.001 TYR B 625 PHE 0.012 0.001 PHE A 57 TRP 0.009 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00301 (14084) covalent geometry : angle 0.53540 (19150) SS BOND : bond 0.00327 ( 10) SS BOND : angle 0.95287 ( 20) hydrogen bonds : bond 0.04026 ( 451) hydrogen bonds : angle 4.63908 ( 1275) link_NAG-ASN : bond 0.00433 ( 8) link_NAG-ASN : angle 2.03473 ( 24) *********************** 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 277 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 235 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: A 274 TYR cc_start: 0.8401 (t80) cc_final: 0.8196 (t80) REVERT: A 490 GLU cc_start: 0.7447 (tt0) cc_final: 0.7215 (tt0) REVERT: A 679 ASN cc_start: 0.7898 (t0) cc_final: 0.7589 (t160) REVERT: B 189 GLU cc_start: 0.6687 (pp20) cc_final: 0.6338 (pp20) REVERT: B 304 VAL cc_start: 0.7188 (OUTLIER) cc_final: 0.6776 (p) REVERT: B 336 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: B 445 LYS cc_start: 0.7674 (tttt) cc_final: 0.7445 (tttm) REVERT: H 188 SER cc_start: 0.8423 (m) cc_final: 0.7869 (t) REVERT: H 212 TYR cc_start: 0.8077 (m-80) cc_final: 0.7830 (m-10) outliers start: 42 outliers final: 26 residues processed: 257 average time/residue: 0.5469 time to fit residues: 154.6545 Evaluate side-chains 261 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 510 LYS 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 336 GLN Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 517 THR 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 166 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 166 SER Chi-restraints excluded: chain H residue 238 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 754 GLN B 99 ASN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126025 restraints weight = 18492.785| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.78 r_work: 0.3632 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1552 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= 0.150 Angle : 0.567 8.199 19194 Z= 0.301 Chirality : 0.045 0.287 2032 Planarity : 0.004 0.045 2428 Dihedral : 5.382 59.136 2056 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.54 % Allowed : 15.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1674 helix: 0.62 (0.36), residues: 232 sheet: 0.45 (0.23), residues: 482 loop : -1.16 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 480 TYR 0.019 0.002 TYR B 113 PHE 0.013 0.002 PHE A 368 TRP 0.012 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00352 (14084) covalent geometry : angle 0.56166 (19150) SS BOND : bond 0.00369 ( 10) SS BOND : angle 0.98244 ( 20) hydrogen bonds : bond 0.04281 ( 451) hydrogen bonds : angle 4.67646 ( 1275) link_NAG-ASN : bond 0.00447 ( 8) link_NAG-ASN : angle 2.03602 ( 24) *********************** 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 274 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7454 (mtp180) REVERT: A 336 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: A 394 LYS cc_start: 0.6878 (tppp) cc_final: 0.6625 (tppp) REVERT: A 679 ASN cc_start: 0.7910 (t0) cc_final: 0.7609 (t160) REVERT: B 189 GLU cc_start: 0.6600 (pp20) cc_final: 0.6257 (pp20) REVERT: B 304 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6765 (p) REVERT: B 336 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: B 445 LYS cc_start: 0.7674 (tttt) cc_final: 0.7450 (tttm) REVERT: H 188 SER cc_start: 0.8429 (m) cc_final: 0.7878 (t) REVERT: H 212 TYR cc_start: 0.8080 (m-80) cc_final: 0.7843 (m-10) outliers start: 37 outliers final: 29 residues processed: 254 average time/residue: 0.5557 time to fit residues: 155.4067 Evaluate side-chains 267 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 363 SER 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 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 510 LYS Chi-restraints excluded: chain B residue 517 THR 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 166 SER 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 166 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 Chi-restraints excluded: chain H residue 238 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 0.0170 chunk 115 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN A 754 GLN B 99 ASN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126466 restraints weight = 18649.199| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.79 r_work: 0.3639 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1598 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= 0.131 Angle : 0.553 7.171 19194 Z= 0.293 Chirality : 0.045 0.278 2032 Planarity : 0.004 0.043 2428 Dihedral : 5.347 58.186 2056 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.67 % Allowed : 15.43 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1674 helix: 0.63 (0.36), residues: 232 sheet: 0.39 (0.22), residues: 516 loop : -1.20 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 480 TYR 0.017 0.001 TYR B 625 PHE 0.015 0.001 PHE H 227 TRP 0.013 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00304 (14084) covalent geometry : angle 0.54845 (19150) SS BOND : bond 0.00311 ( 10) SS BOND : angle 0.92128 ( 20) hydrogen bonds : bond 0.04019 ( 451) hydrogen bonds : angle 4.63250 ( 1275) link_NAG-ASN : bond 0.00420 ( 8) link_NAG-ASN : angle 1.98973 ( 24) *********************** 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 279 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 TYR cc_start: 0.8399 (t80) cc_final: 0.8189 (t80) REVERT: A 317 VAL cc_start: 0.7845 (t) cc_final: 0.7501 (p) REVERT: A 336 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: A 394 LYS cc_start: 0.6948 (tppp) cc_final: 0.6724 (tppp) REVERT: A 679 ASN cc_start: 0.7900 (t0) cc_final: 0.7596 (t160) REVERT: B 189 GLU cc_start: 0.6660 (pp20) cc_final: 0.6312 (pp20) REVERT: B 274 TYR cc_start: 0.8153 (t80) cc_final: 0.7950 (t80) REVERT: B 304 VAL cc_start: 0.7153 (OUTLIER) cc_final: 0.6741 (p) REVERT: B 336 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: B 445 LYS cc_start: 0.7674 (tttt) cc_final: 0.7448 (tttm) REVERT: H 188 SER cc_start: 0.8416 (m) cc_final: 0.7864 (t) REVERT: H 212 TYR cc_start: 0.8062 (m-80) cc_final: 0.7823 (m-10) outliers start: 39 outliers final: 29 residues processed: 258 average time/residue: 0.5195 time to fit residues: 147.8581 Evaluate side-chains 268 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain A residue 336 GLN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 510 LYS 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 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 166 SER 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 166 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 238 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 0.0030 chunk 157 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 496 ASN A 754 GLN B 99 ASN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128405 restraints weight = 18577.690| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.78 r_work: 0.3664 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1656 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= 0.096 Angle : 0.516 7.984 19194 Z= 0.275 Chirality : 0.044 0.275 2032 Planarity : 0.003 0.039 2428 Dihedral : 5.178 57.382 2056 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.19 % Allowed : 16.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.21), residues: 1674 helix: 0.58 (0.36), residues: 238 sheet: 0.35 (0.22), residues: 534 loop : -1.12 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 480 TYR 0.019 0.001 TYR B 625 PHE 0.013 0.001 PHE H 227 TRP 0.016 0.001 TRP A 122 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00212 (14084) covalent geometry : angle 0.51180 (19150) SS BOND : bond 0.00226 ( 10) SS BOND : angle 0.83214 ( 20) hydrogen bonds : bond 0.03394 ( 451) hydrogen bonds : angle 4.56937 ( 1275) link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 1.90195 ( 24) ********************** 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 264 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 TYR cc_start: 0.8412 (t80) cc_final: 0.8196 (t80) REVERT: A 296 LEU cc_start: 0.8081 (tp) cc_final: 0.7865 (tt) REVERT: A 317 VAL cc_start: 0.8065 (t) cc_final: 0.7716 (p) REVERT: A 679 ASN cc_start: 0.7909 (t0) cc_final: 0.7616 (t160) REVERT: B 189 GLU cc_start: 0.6658 (pp20) cc_final: 0.6310 (pp20) REVERT: B 274 TYR cc_start: 0.8193 (t80) cc_final: 0.7968 (t80) REVERT: B 304 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6732 (p) REVERT: B 336 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: B 445 LYS cc_start: 0.7683 (tttt) cc_final: 0.7459 (tttm) REVERT: H 188 SER cc_start: 0.8408 (m) cc_final: 0.7849 (t) outliers start: 32 outliers final: 26 residues processed: 246 average time/residue: 0.5477 time to fit residues: 148.5469 Evaluate side-chains 258 residues out of total 1458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 510 LYS 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 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 166 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 166 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 B 99 ASN B 691 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.139068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125728 restraints weight = 18738.152| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.80 r_work: 0.3629 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14102 Z= 0.168 Angle : 0.585 8.379 19194 Z= 0.310 Chirality : 0.046 0.280 2032 Planarity : 0.004 0.046 2428 Dihedral : 5.403 57.291 2056 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.19 % Allowed : 16.39 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1674 helix: 0.63 (0.36), residues: 232 sheet: 0.45 (0.22), residues: 508 loop : -1.20 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 480 TYR 0.021 0.002 TYR B 113 PHE 0.015 0.002 PHE H 227 TRP 0.015 0.001 TRP A 327 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00399 (14084) covalent geometry : angle 0.58070 (19150) SS BOND : bond 0.00421 ( 10) SS BOND : angle 1.01144 ( 20) hydrogen bonds : bond 0.04414 ( 451) hydrogen bonds : angle 4.69649 ( 1275) link_NAG-ASN : bond 0.00430 ( 8) link_NAG-ASN : angle 2.00161 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5011.01 seconds wall clock time: 86 minutes 9.36 seconds (5169.36 seconds total)