Starting phenix.real_space_refine on Thu May 15 07:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvq_47215/05_2025/9dvq_47215.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 48 5.16 5 C 8252 2.51 5 N 2086 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12791 Number of models: 1 Model: "" Number of chains: 5 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.80, per 1000 atoms: 0.61 Number of scatterers: 12791 At special positions: 0 Unit cell: (88.58, 121.26, 154.8, 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 48 16.00 O 2405 8.00 N 2086 7.00 C 8252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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=2.20 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=2.17 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 227 " " NAG A 802 " - " ASN A 92 " " NAG A 803 " - " ASN A 49 " " NAG A 804 " - " ASN A 314 " " NAG B 801 " - " ASN B 227 " " NAG B 802 " - " ASN B 92 " " NAG B 803 " - " ASN B 49 " " NAG B 804 " - " ASN B 314 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 26 sheets defined 19.9% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.516A pdb=" N MET A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.914A 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 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.539A pdb=" N TYR A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 491 through 498 removed outlier: 3.508A 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 Processing helix chain 'A' and resid 594 through 611 removed outlier: 3.820A pdb=" N GLU A 598 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.904A 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: 3.734A pdb=" N TYR A 656 " --> pdb=" O TRP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 removed outlier: 3.756A pdb=" N PHE A 664 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 680 through 681 No H-bonds generated for 'chain 'A' and resid 680 through 681' Processing helix chain 'A' and resid 682 through 690 removed outlier: 5.065A pdb=" N GLU A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 689 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.755A 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 756 removed outlier: 4.219A pdb=" N ASN A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.815A pdb=" N VAL B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 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 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.623A 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 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 594 through 611 removed outlier: 3.739A pdb=" N GLU B 598 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 removed outlier: 3.701A pdb=" N VAL B 629 " --> pdb=" O TYR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.606A pdb=" N ARG B 663 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 664 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 680 removed outlier: 3.695A pdb=" N LYS B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 679 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 680 " --> pdb=" O HIS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 690 removed outlier: 5.118A pdb=" N GLU B 687 " --> pdb=" O ALA B 684 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 689 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 738 through 756 removed outlier: 4.150A 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: 3.616A pdb=" N ASN A 60 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 90 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 78 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N THR A 88 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN A 80 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 5.835A 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: 3.523A pdb=" N ASN A 102 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR A 118 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.818A 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 155 removed outlier: 3.804A 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: 3.582A pdb=" N LEU A 309 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 307 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 296 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 305 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP A 298 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG A 303 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.132A 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: 3.582A pdb=" N LEU A 309 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 307 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 296 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 305 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP A 298 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG A 303 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.132A 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 Processing sheet with id=AB1, first strand: chain 'A' and resid 397 through 403 removed outlier: 6.297A pdb=" N ILE A 400 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER A 411 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 402 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N SER A 435 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 448 through 455 removed outlier: 6.733A pdb=" N GLY A 468 " --> pdb=" O GLN A 449 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR A 451 " --> pdb=" O CYS A 466 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS A 466 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 453 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 464 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE A 455 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A 462 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 462 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 476 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 5.890A 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: 4.834A pdb=" N VAL A 572 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR A 534 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 616 " --> pdb=" O TYR A 534 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU A 536 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 618 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 538 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 620 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 540 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A 622 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS A 643 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 618 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE A 645 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 620 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL A 647 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY A 622 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 694 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N MET A 727 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 696 " --> pdb=" O MET A 727 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N TYR A 729 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 7.034A 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: 3.590A pdb=" N ASN B 60 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 90 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU B 78 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR B 88 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASN B 80 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER B 86 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.578A pdb=" N ASN B 102 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR B 118 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.720A 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 155 removed outlier: 3.722A 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: 6.586A pdb=" N GLN B 307 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 296 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS B 305 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TRP B 298 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG B 303 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 5.693A 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: 6.586A pdb=" N GLN B 307 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 296 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS B 305 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TRP B 298 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ARG B 303 " --> pdb=" O TRP B 298 " (cutoff:3.500A) removed outlier: 5.693A 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: 6.221A pdb=" N ILE B 400 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER B 411 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 402 " --> pdb=" O PHE B 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 448 through 455 removed outlier: 6.813A pdb=" N GLY B 468 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR B 451 " --> pdb=" O CYS B 466 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS B 466 " --> pdb=" O TYR B 451 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 453 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 464 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B 455 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 462 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 476 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE B 487 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP B 478 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 7.909A 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: 4.608A pdb=" N VAL B 572 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 534 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS B 616 " --> pdb=" O TYR B 534 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU B 536 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 618 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 538 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 620 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 540 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY B 622 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS B 643 " --> pdb=" O LYS B 616 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 618 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ILE B 645 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 620 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL B 647 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY B 622 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.608A pdb=" N GLN G 120 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 127 through 129 removed outlier: 5.994A pdb=" N GLY G 127 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG G 155 " --> pdb=" O TRP G 164 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP G 164 " --> pdb=" O ARG G 155 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1179 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: 4.46 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3978 1.34 - 1.46: 3442 1.46 - 1.58: 5662 1.58 - 1.70: 9 1.70 - 1.81: 72 Bond restraints: 13163 Sorted by residual: bond pdb=" C7 NAG B 804 " pdb=" N2 NAG B 804 " ideal model delta sigma weight residual 1.346 1.410 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 NAG B 804 " pdb=" C3 NAG B 804 " ideal model delta sigma weight residual 1.526 1.589 -0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" C7 NAG A 803 " pdb=" N2 NAG A 803 " ideal model delta sigma weight residual 1.346 1.405 -0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" C7 NAG B 802 " pdb=" N2 NAG B 802 " ideal model delta sigma weight residual 1.346 1.405 -0.059 2.00e-02 2.50e+03 8.71e+00 bond pdb=" C1 NAG B 804 " pdb=" C2 NAG B 804 " ideal model delta sigma weight residual 1.532 1.590 -0.058 2.00e-02 2.50e+03 8.48e+00 ... (remaining 13158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 17533 1.77 - 3.55: 284 3.55 - 5.32: 68 5.32 - 7.10: 15 7.10 - 8.87: 1 Bond angle restraints: 17901 Sorted by residual: angle pdb=" CB LYS B 371 " pdb=" CG LYS B 371 " pdb=" CD LYS B 371 " ideal model delta sigma weight residual 111.30 120.17 -8.87 2.30e+00 1.89e-01 1.49e+01 angle pdb=" C CYS A 755 " pdb=" CA CYS A 755 " pdb=" CB CYS A 755 " ideal model delta sigma weight residual 110.85 104.74 6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" C SER B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.47 123.06 -3.59 1.16e+00 7.43e-01 9.58e+00 angle pdb=" CA ASP B 108 " pdb=" CB ASP B 108 " pdb=" CG ASP B 108 " ideal model delta sigma weight residual 112.60 115.66 -3.06 1.00e+00 1.00e+00 9.34e+00 angle pdb=" CA ASP B 178 " pdb=" CB ASP B 178 " pdb=" CG ASP B 178 " ideal model delta sigma weight residual 112.60 115.52 -2.92 1.00e+00 1.00e+00 8.53e+00 ... (remaining 17896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 6808 17.43 - 34.86: 723 34.86 - 52.29: 212 52.29 - 69.73: 45 69.73 - 87.16: 15 Dihedral angle restraints: 7803 sinusoidal: 3201 harmonic: 4602 Sorted by residual: dihedral pdb=" CB CYS B 438 " pdb=" SG CYS B 438 " pdb=" SG CYS B 441 " pdb=" CB CYS B 441 " ideal model delta sinusoidal sigma weight residual -86.00 -172.64 86.64 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS A 438 " pdb=" SG CYS A 438 " pdb=" SG CYS A 441 " pdb=" CB CYS A 441 " ideal model delta sinusoidal sigma weight residual -86.00 -165.95 79.95 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CD ARG B 175 " pdb=" NE ARG B 175 " pdb=" CZ ARG B 175 " pdb=" NH1 ARG B 175 " ideal model delta sinusoidal sigma weight residual 0.00 -46.86 46.86 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 7800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1802 0.105 - 0.210: 79 0.210 - 0.315: 8 0.315 - 0.420: 7 0.420 - 0.524: 1 Chirality restraints: 1897 Sorted by residual: 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 -3.02 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C2 NAG A 803 " pdb=" C1 NAG A 803 " pdb=" C3 NAG A 803 " pdb=" N2 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.49 -2.91 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C2 NAG B 803 " pdb=" C1 NAG B 803 " pdb=" C3 NAG B 803 " pdb=" N2 NAG B 803 " both_signs ideal model delta sigma weight residual False -2.49 -2.90 0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 1894 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 175 " 0.797 9.50e-02 1.11e+02 3.57e-01 7.77e+01 pdb=" NE ARG B 175 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG B 175 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 175 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 175 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 227 " -0.015 2.00e-02 2.50e+03 1.06e-02 1.98e+00 pdb=" CG PHE G 227 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE G 227 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE G 227 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 227 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE G 227 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 148 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 149 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.017 5.00e-02 4.00e+02 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 162 2.67 - 3.23: 10732 3.23 - 3.78: 17910 3.78 - 4.34: 26414 4.34 - 4.90: 44415 Nonbonded interactions: 99633 Sorted by model distance: nonbonded pdb=" NH2 ARG B 590 " pdb=" C8 NAG B 804 " model vdw 2.109 3.540 nonbonded pdb=" OD1 ASN A 259 " pdb=" NH1 ARG A 311 " model vdw 2.160 3.120 nonbonded pdb=" O GLY A 626 " pdb=" OG SER A 630 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 342 " pdb=" O GLY A 345 " model vdw 2.222 3.040 nonbonded pdb=" N GLU A 189 " pdb=" OE1 GLU A 189 " model vdw 2.239 3.120 ... (remaining 99628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.460 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 13180 Z= 0.247 Angle : 0.659 22.385 17943 Z= 0.345 Chirality : 0.055 0.524 1897 Planarity : 0.008 0.357 2268 Dihedral : 16.041 87.157 4856 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.81 % Allowed : 18.27 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1554 helix: 0.64 (0.36), residues: 232 sheet: 0.42 (0.23), residues: 498 loop : -1.20 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.004 0.001 HIS B 698 PHE 0.023 0.001 PHE G 227 TYR 0.017 0.001 TYR A 113 ARG 0.002 0.000 ARG A 343 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 8) link_NAG-ASN : angle 2.61298 ( 24) hydrogen bonds : bond 0.14480 ( 420) hydrogen bonds : angle 6.34264 ( 1179) SS BOND : bond 0.07341 ( 9) SS BOND : angle 7.70005 ( 18) covalent geometry : bond 0.00469 (13163) covalent geometry : angle 0.60566 (17901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 281 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7283 (mm-30) REVERT: A 350 PHE cc_start: 0.7705 (t80) cc_final: 0.7399 (t80) REVERT: A 392 SER cc_start: 0.7776 (p) cc_final: 0.7410 (m) REVERT: A 446 GLU cc_start: 0.7591 (mp0) cc_final: 0.7222 (mp0) REVERT: A 458 TYR cc_start: 0.8157 (m-80) cc_final: 0.7920 (m-80) REVERT: A 507 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7612 (mm-30) REVERT: A 679 ASN cc_start: 0.6660 (t0) cc_final: 0.6414 (t0) REVERT: B 45 LYS cc_start: 0.7133 (mttm) cc_final: 0.6842 (mtmm) REVERT: B 54 TYR cc_start: 0.7901 (p90) cc_final: 0.7685 (p90) REVERT: B 95 MET cc_start: 0.6574 (mmm) cc_final: 0.6273 (mmm) REVERT: B 118 TYR cc_start: 0.8080 (t80) cc_final: 0.7839 (t80) REVERT: B 172 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7158 (tp) REVERT: B 175 ARG cc_start: 0.7013 (mtm180) cc_final: 0.6811 (ptp-110) REVERT: B 288 SER cc_start: 0.7488 (m) cc_final: 0.7231 (p) REVERT: B 302 GLU cc_start: 0.7392 (mp0) cc_final: 0.7178 (mp0) REVERT: B 316 SER cc_start: 0.7833 (t) cc_final: 0.7624 (p) REVERT: B 325 GLU cc_start: 0.6705 (tp30) cc_final: 0.6484 (tp30) REVERT: B 371 LYS cc_start: 0.7493 (mttt) cc_final: 0.7258 (mttt) REVERT: B 372 ASP cc_start: 0.7180 (m-30) cc_final: 0.6955 (m-30) REVERT: B 394 LYS cc_start: 0.7828 (tppt) cc_final: 0.7561 (tppp) REVERT: B 435 SER cc_start: 0.7912 (t) cc_final: 0.7677 (t) REVERT: B 437 LYS cc_start: 0.7476 (tttt) cc_final: 0.7227 (ttmt) REVERT: B 458 TYR cc_start: 0.7710 (m-80) cc_final: 0.7065 (m-80) REVERT: B 483 GLN cc_start: 0.7183 (pt0) cc_final: 0.6813 (pt0) REVERT: B 490 GLU cc_start: 0.8144 (pt0) cc_final: 0.7906 (pt0) REVERT: B 502 GLN cc_start: 0.7763 (pt0) cc_final: 0.7521 (pt0) REVERT: B 573 ASP cc_start: 0.7414 (m-30) cc_final: 0.7144 (m-30) REVERT: B 591 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7651 (mtpp) REVERT: B 687 GLU cc_start: 0.7876 (tp30) cc_final: 0.7185 (tp30) outliers start: 11 outliers final: 7 residues processed: 289 average time/residue: 1.3583 time to fit residues: 422.7174 Evaluate side-chains 268 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 643 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 496 ASN A 676 HIS B 74 ASN B 500 ASN B 709 ASN B 742 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.082252 restraints weight = 18616.208| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.60 r_work: 0.2844 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 13180 Z= 0.269 Angle : 0.678 9.896 17943 Z= 0.362 Chirality : 0.051 0.423 1897 Planarity : 0.005 0.046 2268 Dihedral : 6.032 56.710 1929 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.93 % Allowed : 17.17 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1554 helix: 0.14 (0.34), residues: 236 sheet: 0.66 (0.23), residues: 473 loop : -1.35 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 298 HIS 0.007 0.002 HIS A 676 PHE 0.027 0.002 PHE G 227 TYR 0.026 0.002 TYR B 87 ARG 0.009 0.001 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 3.27054 ( 24) hydrogen bonds : bond 0.06273 ( 420) hydrogen bonds : angle 5.13784 ( 1179) SS BOND : bond 0.00500 ( 9) SS BOND : angle 1.74169 ( 18) covalent geometry : bond 0.00686 (13163) covalent geometry : angle 0.66608 (17901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 332 CYS cc_start: 0.7459 (m) cc_final: 0.7074 (m) REVERT: A 350 PHE cc_start: 0.8758 (t80) cc_final: 0.8371 (t80) REVERT: A 446 GLU cc_start: 0.8027 (mp0) cc_final: 0.7802 (mp0) REVERT: A 458 TYR cc_start: 0.8706 (m-80) cc_final: 0.8492 (m-80) REVERT: A 483 GLN cc_start: 0.8217 (tp40) cc_final: 0.7767 (tp40) REVERT: A 679 ASN cc_start: 0.7983 (t0) cc_final: 0.7623 (t0) REVERT: B 66 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 95 MET cc_start: 0.8588 (mmm) cc_final: 0.8361 (mmm) REVERT: B 458 TYR cc_start: 0.8315 (m-80) cc_final: 0.7726 (m-80) REVERT: B 483 GLN cc_start: 0.8273 (pt0) cc_final: 0.8030 (pt0) REVERT: B 493 GLU cc_start: 0.7452 (pm20) cc_final: 0.7243 (pm20) REVERT: B 502 GLN cc_start: 0.8668 (pt0) cc_final: 0.8447 (pt0) REVERT: B 687 GLU cc_start: 0.8047 (tp30) cc_final: 0.7761 (tp30) outliers start: 40 outliers final: 17 residues processed: 293 average time/residue: 1.4211 time to fit residues: 447.5885 Evaluate side-chains 281 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 218 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 95 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 0.0030 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 386 ASN A 496 ASN A 712 GLN B 74 ASN B 80 ASN B 500 ASN B 709 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.084136 restraints weight = 18761.571| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.63 r_work: 0.2878 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13180 Z= 0.131 Angle : 0.554 7.976 17943 Z= 0.300 Chirality : 0.046 0.357 1897 Planarity : 0.004 0.040 2268 Dihedral : 5.477 55.429 1918 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.57 % Allowed : 18.49 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1554 helix: 0.31 (0.34), residues: 236 sheet: 0.73 (0.23), residues: 473 loop : -1.25 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 122 HIS 0.002 0.001 HIS B 747 PHE 0.023 0.001 PHE G 227 TYR 0.017 0.001 TYR A 113 ARG 0.009 0.000 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 8) link_NAG-ASN : angle 2.83798 ( 24) hydrogen bonds : bond 0.04688 ( 420) hydrogen bonds : angle 4.88258 ( 1179) SS BOND : bond 0.00486 ( 9) SS BOND : angle 1.67207 ( 18) covalent geometry : bond 0.00314 (13163) covalent geometry : angle 0.54212 (17901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8540 (mt) cc_final: 0.8320 (mt) REVERT: A 148 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7513 (ptm160) REVERT: A 350 PHE cc_start: 0.8758 (t80) cc_final: 0.8431 (t80) REVERT: A 446 GLU cc_start: 0.8003 (mp0) cc_final: 0.7761 (mp0) REVERT: A 483 GLN cc_start: 0.8241 (tp40) cc_final: 0.7820 (tp40) REVERT: B 66 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 88 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8344 (t) REVERT: B 95 MET cc_start: 0.8574 (mmm) cc_final: 0.8196 (mmm) REVERT: B 148 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8114 (ttm110) REVERT: B 359 TYR cc_start: 0.7962 (t80) cc_final: 0.7710 (t80) REVERT: B 458 TYR cc_start: 0.8268 (m-80) cc_final: 0.7715 (m-80) REVERT: B 483 GLN cc_start: 0.8262 (pt0) cc_final: 0.8026 (pt0) REVERT: B 502 GLN cc_start: 0.8587 (pt0) cc_final: 0.8369 (pt0) REVERT: B 687 GLU cc_start: 0.8071 (tp30) cc_final: 0.7764 (tp30) outliers start: 35 outliers final: 24 residues processed: 285 average time/residue: 1.4599 time to fit residues: 447.6528 Evaluate side-chains 287 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 260 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 386 ASN A 496 ASN B 74 ASN B 328 GLN B 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084168 restraints weight = 18562.044| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.62 r_work: 0.2880 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13180 Z= 0.136 Angle : 0.551 7.699 17943 Z= 0.298 Chirality : 0.046 0.354 1897 Planarity : 0.004 0.040 2268 Dihedral : 5.319 54.980 1918 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.57 % Allowed : 18.86 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.21), residues: 1554 helix: 0.40 (0.35), residues: 236 sheet: 0.70 (0.23), residues: 485 loop : -1.26 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.001 HIS A 747 PHE 0.024 0.001 PHE G 227 TYR 0.019 0.002 TYR A 113 ARG 0.004 0.000 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 2.80611 ( 24) hydrogen bonds : bond 0.04612 ( 420) hydrogen bonds : angle 4.81083 ( 1179) SS BOND : bond 0.00417 ( 9) SS BOND : angle 1.50260 ( 18) covalent geometry : bond 0.00330 (13163) covalent geometry : angle 0.53972 (17901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8534 (mt) cc_final: 0.8311 (mt) REVERT: A 148 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7609 (ptm160) REVERT: A 332 CYS cc_start: 0.7353 (m) cc_final: 0.7001 (m) REVERT: A 350 PHE cc_start: 0.8730 (t80) cc_final: 0.8387 (t80) REVERT: A 404 THR cc_start: 0.8460 (t) cc_final: 0.8182 (p) REVERT: A 446 GLU cc_start: 0.8003 (mp0) cc_final: 0.7758 (mp0) REVERT: A 483 GLN cc_start: 0.8233 (tp40) cc_final: 0.7808 (tp40) REVERT: B 66 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8301 (mt-10) REVERT: B 88 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8356 (t) REVERT: B 95 MET cc_start: 0.8571 (mmm) cc_final: 0.8180 (mmm) REVERT: B 139 GLU cc_start: 0.7279 (pm20) cc_final: 0.7011 (pt0) REVERT: B 148 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8096 (ttm110) REVERT: B 231 ILE cc_start: 0.8442 (mt) cc_final: 0.8232 (mp) REVERT: B 359 TYR cc_start: 0.7948 (t80) cc_final: 0.7690 (t80) REVERT: B 402 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7360 (tpp-160) REVERT: B 458 TYR cc_start: 0.8266 (m-80) cc_final: 0.7782 (m-80) REVERT: B 483 GLN cc_start: 0.8246 (pt0) cc_final: 0.8023 (pt0) REVERT: B 502 GLN cc_start: 0.8576 (pt0) cc_final: 0.8360 (pt0) REVERT: B 617 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.6819 (mtt180) REVERT: B 687 GLU cc_start: 0.8045 (tp30) cc_final: 0.7668 (tp30) outliers start: 35 outliers final: 20 residues processed: 281 average time/residue: 1.4026 time to fit residues: 422.7857 Evaluate side-chains 286 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 128 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 190 ASN A 386 ASN A 496 ASN B 74 ASN B 328 GLN B 405 GLN B 500 ASN B 709 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.084020 restraints weight = 18737.781| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.63 r_work: 0.2880 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13180 Z= 0.147 Angle : 0.559 8.095 17943 Z= 0.302 Chirality : 0.046 0.357 1897 Planarity : 0.004 0.040 2268 Dihedral : 5.303 55.929 1918 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.23 % Allowed : 18.86 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1554 helix: 0.41 (0.35), residues: 236 sheet: 0.71 (0.23), residues: 485 loop : -1.27 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.002 0.001 HIS A 747 PHE 0.024 0.001 PHE G 227 TYR 0.020 0.002 TYR A 113 ARG 0.005 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 2.82741 ( 24) hydrogen bonds : bond 0.04749 ( 420) hydrogen bonds : angle 4.79171 ( 1179) SS BOND : bond 0.00383 ( 9) SS BOND : angle 1.58257 ( 18) covalent geometry : bond 0.00362 (13163) covalent geometry : angle 0.54756 (17901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8525 (mt) cc_final: 0.8296 (mt) REVERT: A 148 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7645 (ptm160) REVERT: A 332 CYS cc_start: 0.7387 (m) cc_final: 0.6986 (m) REVERT: A 350 PHE cc_start: 0.8721 (t80) cc_final: 0.8423 (t80) REVERT: A 404 THR cc_start: 0.8477 (t) cc_final: 0.8216 (p) REVERT: A 446 GLU cc_start: 0.8010 (mp0) cc_final: 0.7765 (mp0) REVERT: A 483 GLN cc_start: 0.8225 (tp40) cc_final: 0.7804 (tp40) REVERT: B 66 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 88 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (t) REVERT: B 95 MET cc_start: 0.8569 (mmm) cc_final: 0.8272 (mmm) REVERT: B 139 GLU cc_start: 0.7302 (pm20) cc_final: 0.7072 (pt0) REVERT: B 148 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8109 (ttm110) REVERT: B 231 ILE cc_start: 0.8455 (mt) cc_final: 0.8243 (mp) REVERT: B 402 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7393 (tpp-160) REVERT: B 458 TYR cc_start: 0.8266 (m-80) cc_final: 0.7797 (m-80) REVERT: B 483 GLN cc_start: 0.8219 (pt0) cc_final: 0.7996 (pt0) REVERT: B 502 GLN cc_start: 0.8579 (pt0) cc_final: 0.8357 (pt0) REVERT: B 617 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.6793 (mtt180) REVERT: G 166 SER cc_start: 0.7981 (t) cc_final: 0.7758 (t) outliers start: 44 outliers final: 27 residues processed: 288 average time/residue: 1.4538 time to fit residues: 449.2235 Evaluate side-chains 296 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 328 GLN A 386 ASN A 496 ASN B 74 ASN B 174 GLN B 328 GLN B 500 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.083447 restraints weight = 18828.762| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.62 r_work: 0.2865 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13180 Z= 0.198 Angle : 0.618 11.783 17943 Z= 0.330 Chirality : 0.048 0.372 1897 Planarity : 0.004 0.040 2268 Dihedral : 5.479 57.566 1918 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.23 % Allowed : 18.78 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1554 helix: 0.30 (0.34), residues: 236 sheet: 0.72 (0.23), residues: 473 loop : -1.34 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 327 HIS 0.003 0.001 HIS A 477 PHE 0.027 0.002 PHE G 227 TYR 0.023 0.002 TYR A 113 ARG 0.005 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 2.97062 ( 24) hydrogen bonds : bond 0.05473 ( 420) hydrogen bonds : angle 4.92313 ( 1179) SS BOND : bond 0.00514 ( 9) SS BOND : angle 1.95213 ( 18) covalent geometry : bond 0.00497 (13163) covalent geometry : angle 0.60567 (17901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8497 (mt) cc_final: 0.8253 (mt) REVERT: A 148 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.7748 (ptm160) REVERT: A 313 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7411 (mt0) REVERT: A 332 CYS cc_start: 0.7407 (m) cc_final: 0.7025 (m) REVERT: A 404 THR cc_start: 0.8505 (t) cc_final: 0.8253 (p) REVERT: A 446 GLU cc_start: 0.8037 (mp0) cc_final: 0.7797 (mp0) REVERT: A 483 GLN cc_start: 0.8239 (tp40) cc_final: 0.7817 (tp40) REVERT: B 88 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (t) REVERT: B 95 MET cc_start: 0.8565 (mmm) cc_final: 0.8280 (mmm) REVERT: B 148 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8110 (ttm110) REVERT: B 327 TRP cc_start: 0.7867 (m-10) cc_final: 0.7664 (m-90) REVERT: B 402 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7435 (tpp-160) REVERT: B 458 TYR cc_start: 0.8290 (m-80) cc_final: 0.7816 (m-80) REVERT: B 483 GLN cc_start: 0.8247 (pt0) cc_final: 0.8017 (pt0) REVERT: B 617 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6767 (mtt180) REVERT: B 679 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7810 (m110) REVERT: G 166 SER cc_start: 0.8021 (t) cc_final: 0.7773 (t) outliers start: 44 outliers final: 31 residues processed: 294 average time/residue: 1.4446 time to fit residues: 456.3116 Evaluate side-chains 308 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 643 CYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 120 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 386 ASN A 496 ASN A 721 GLN B 74 ASN B 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.084778 restraints weight = 18580.603| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.62 r_work: 0.2890 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13180 Z= 0.124 Angle : 0.553 11.006 17943 Z= 0.298 Chirality : 0.046 0.353 1897 Planarity : 0.004 0.055 2268 Dihedral : 5.261 57.191 1918 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.15 % Allowed : 19.59 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1554 helix: 0.21 (0.34), residues: 248 sheet: 0.70 (0.23), residues: 485 loop : -1.32 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.002 0.001 HIS B 676 PHE 0.024 0.001 PHE G 227 TYR 0.016 0.001 TYR A 113 ARG 0.012 0.000 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 8) link_NAG-ASN : angle 2.72477 ( 24) hydrogen bonds : bond 0.04399 ( 420) hydrogen bonds : angle 4.75552 ( 1179) SS BOND : bond 0.00375 ( 9) SS BOND : angle 1.50958 ( 18) covalent geometry : bond 0.00298 (13163) covalent geometry : angle 0.54226 (17901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8504 (mt) cc_final: 0.8286 (mt) REVERT: A 148 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7660 (ptm160) REVERT: A 332 CYS cc_start: 0.7386 (m) cc_final: 0.6993 (m) REVERT: A 404 THR cc_start: 0.8484 (t) cc_final: 0.8236 (p) REVERT: A 427 ILE cc_start: 0.8307 (mt) cc_final: 0.8104 (pt) REVERT: A 446 GLU cc_start: 0.8004 (mp0) cc_final: 0.7761 (mp0) REVERT: A 483 GLN cc_start: 0.8223 (tp40) cc_final: 0.7791 (tp40) REVERT: A 564 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (tttt) REVERT: B 88 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8367 (t) REVERT: B 95 MET cc_start: 0.8554 (mmm) cc_final: 0.8247 (mmm) REVERT: B 402 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7395 (tpp-160) REVERT: B 458 TYR cc_start: 0.8262 (m-80) cc_final: 0.7796 (m-80) REVERT: B 483 GLN cc_start: 0.8229 (pt0) cc_final: 0.8016 (pt0) REVERT: B 502 GLN cc_start: 0.8560 (pt0) cc_final: 0.8341 (pt0) REVERT: B 617 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6737 (mtt180) REVERT: G 166 SER cc_start: 0.7967 (t) cc_final: 0.7710 (t) outliers start: 43 outliers final: 26 residues processed: 291 average time/residue: 1.4402 time to fit residues: 451.2555 Evaluate side-chains 296 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 139 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 386 ASN A 496 ASN A 721 GLN B 74 ASN B 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.084437 restraints weight = 18655.726| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.65 r_work: 0.2885 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13180 Z= 0.132 Angle : 0.557 10.801 17943 Z= 0.299 Chirality : 0.046 0.355 1897 Planarity : 0.004 0.048 2268 Dihedral : 5.204 57.030 1918 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.71 % Allowed : 20.10 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1554 helix: 0.23 (0.34), residues: 248 sheet: 0.70 (0.23), residues: 485 loop : -1.31 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 327 HIS 0.002 0.001 HIS A 734 PHE 0.024 0.001 PHE G 227 TYR 0.018 0.001 TYR A 113 ARG 0.011 0.001 ARG A 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 8) link_NAG-ASN : angle 2.69978 ( 24) hydrogen bonds : bond 0.04479 ( 420) hydrogen bonds : angle 4.72347 ( 1179) SS BOND : bond 0.00454 ( 9) SS BOND : angle 1.87121 ( 18) covalent geometry : bond 0.00321 (13163) covalent geometry : angle 0.54542 (17901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8504 (mt) cc_final: 0.8284 (mt) REVERT: A 148 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7637 (ptm160) REVERT: A 332 CYS cc_start: 0.7413 (m) cc_final: 0.7017 (m) REVERT: A 404 THR cc_start: 0.8498 (t) cc_final: 0.8247 (p) REVERT: A 446 GLU cc_start: 0.8025 (mp0) cc_final: 0.7785 (mp0) REVERT: A 483 GLN cc_start: 0.8249 (tp40) cc_final: 0.7814 (tp40) REVERT: A 564 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8364 (tttt) REVERT: B 88 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (t) REVERT: B 95 MET cc_start: 0.8546 (mmm) cc_final: 0.8234 (mmm) REVERT: B 123 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7170 (ttp-170) REVERT: B 402 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7393 (tpp-160) REVERT: B 458 TYR cc_start: 0.8282 (m-80) cc_final: 0.7810 (m-80) REVERT: B 483 GLN cc_start: 0.8235 (pt0) cc_final: 0.8018 (pt0) REVERT: B 502 GLN cc_start: 0.8563 (pt0) cc_final: 0.8343 (pt0) REVERT: B 617 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.6789 (mtt180) REVERT: G 166 SER cc_start: 0.7972 (t) cc_final: 0.7708 (t) outliers start: 37 outliers final: 26 residues processed: 283 average time/residue: 1.4993 time to fit residues: 455.3376 Evaluate side-chains 295 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 386 ASN A 496 ASN A 721 GLN B 74 ASN B 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.084158 restraints weight = 18519.587| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.61 r_work: 0.2881 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13180 Z= 0.170 Angle : 0.592 11.423 17943 Z= 0.318 Chirality : 0.047 0.361 1897 Planarity : 0.004 0.063 2268 Dihedral : 5.303 57.715 1918 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.93 % Allowed : 20.18 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1554 helix: 0.15 (0.34), residues: 248 sheet: 0.73 (0.23), residues: 473 loop : -1.33 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 327 HIS 0.002 0.001 HIS B 376 PHE 0.025 0.002 PHE G 227 TYR 0.021 0.002 TYR A 113 ARG 0.014 0.001 ARG B 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 2.76865 ( 24) hydrogen bonds : bond 0.04994 ( 420) hydrogen bonds : angle 4.79315 ( 1179) SS BOND : bond 0.00472 ( 9) SS BOND : angle 1.85243 ( 18) covalent geometry : bond 0.00426 (13163) covalent geometry : angle 0.58092 (17901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8498 (mt) cc_final: 0.8275 (mt) REVERT: A 148 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7682 (ptm160) REVERT: A 313 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: A 332 CYS cc_start: 0.7407 (m) cc_final: 0.7024 (m) REVERT: A 335 THR cc_start: 0.8844 (t) cc_final: 0.8572 (p) REVERT: A 343 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7995 (mmm-85) REVERT: A 404 THR cc_start: 0.8508 (t) cc_final: 0.8257 (p) REVERT: A 446 GLU cc_start: 0.8030 (mp0) cc_final: 0.7790 (mp0) REVERT: A 483 GLN cc_start: 0.8234 (tp40) cc_final: 0.7800 (tp40) REVERT: B 95 MET cc_start: 0.8543 (mmm) cc_final: 0.8233 (mmm) REVERT: B 123 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7180 (ttt180) REVERT: B 231 ILE cc_start: 0.8493 (mt) cc_final: 0.8226 (mp) REVERT: B 402 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7403 (tpp-160) REVERT: B 458 TYR cc_start: 0.8284 (m-80) cc_final: 0.7822 (m-80) REVERT: B 483 GLN cc_start: 0.8228 (pt0) cc_final: 0.8011 (pt0) REVERT: B 502 GLN cc_start: 0.8585 (pt0) cc_final: 0.8367 (pt0) REVERT: B 617 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.6744 (mtt180) REVERT: B 679 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7816 (m110) REVERT: G 166 SER cc_start: 0.8003 (t) cc_final: 0.7740 (t) outliers start: 40 outliers final: 28 residues processed: 291 average time/residue: 1.4510 time to fit residues: 453.4275 Evaluate side-chains 298 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 132 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 386 ASN A 496 ASN A 721 GLN B 74 ASN B 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.083865 restraints weight = 18536.051| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.61 r_work: 0.2875 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13180 Z= 0.181 Angle : 0.604 11.445 17943 Z= 0.324 Chirality : 0.048 0.364 1897 Planarity : 0.005 0.071 2268 Dihedral : 5.379 58.559 1918 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.79 % Allowed : 20.32 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1554 helix: 0.11 (0.33), residues: 248 sheet: 0.70 (0.23), residues: 473 loop : -1.36 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 327 HIS 0.003 0.001 HIS B 376 PHE 0.026 0.002 PHE G 227 TYR 0.021 0.002 TYR A 113 ARG 0.014 0.001 ARG B 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 8) link_NAG-ASN : angle 2.76405 ( 24) hydrogen bonds : bond 0.05162 ( 420) hydrogen bonds : angle 4.84669 ( 1179) SS BOND : bond 0.00485 ( 9) SS BOND : angle 1.82624 ( 18) covalent geometry : bond 0.00453 (13163) covalent geometry : angle 0.59367 (17901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8491 (mt) cc_final: 0.8262 (mt) REVERT: A 148 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7730 (ptm160) REVERT: A 313 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7385 (mt0) REVERT: A 332 CYS cc_start: 0.7463 (m) cc_final: 0.7079 (m) REVERT: A 335 THR cc_start: 0.8830 (t) cc_final: 0.8562 (p) REVERT: A 343 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: A 404 THR cc_start: 0.8516 (t) cc_final: 0.8263 (p) REVERT: A 446 GLU cc_start: 0.8053 (mp0) cc_final: 0.7815 (mp0) REVERT: A 483 GLN cc_start: 0.8239 (tp40) cc_final: 0.7801 (tp40) REVERT: A 564 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8376 (tttt) REVERT: B 95 MET cc_start: 0.8548 (mmm) cc_final: 0.8241 (mmm) REVERT: B 123 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7239 (ttt180) REVERT: B 148 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8061 (ptp-170) REVERT: B 231 ILE cc_start: 0.8474 (mt) cc_final: 0.8241 (mp) REVERT: B 402 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7443 (tpp-160) REVERT: B 458 TYR cc_start: 0.8293 (m-80) cc_final: 0.7809 (m-80) REVERT: B 483 GLN cc_start: 0.8233 (pt0) cc_final: 0.8013 (pt0) REVERT: B 502 GLN cc_start: 0.8602 (pt0) cc_final: 0.8383 (pt0) REVERT: B 617 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.6743 (mtt180) REVERT: B 679 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (m110) REVERT: G 166 SER cc_start: 0.7996 (t) cc_final: 0.7736 (t) outliers start: 38 outliers final: 25 residues processed: 288 average time/residue: 1.4223 time to fit residues: 440.0524 Evaluate side-chains 299 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 466 CYS Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 755 CYS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 679 ASN Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 152 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 82 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 386 ASN A 496 ASN A 721 GLN B 74 ASN B 500 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.085784 restraints weight = 18508.979| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.61 r_work: 0.2911 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13180 Z= 0.103 Angle : 0.522 10.378 17943 Z= 0.282 Chirality : 0.045 0.344 1897 Planarity : 0.004 0.062 2268 Dihedral : 5.057 56.581 1918 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.20 % Allowed : 20.91 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1554 helix: 0.29 (0.34), residues: 248 sheet: 0.73 (0.23), residues: 485 loop : -1.30 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 327 HIS 0.002 0.001 HIS A 747 PHE 0.022 0.001 PHE G 227 TYR 0.014 0.001 TYR B 113 ARG 0.014 0.001 ARG B 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 2.46491 ( 24) hydrogen bonds : bond 0.03846 ( 420) hydrogen bonds : angle 4.61639 ( 1179) SS BOND : bond 0.00345 ( 9) SS BOND : angle 1.48292 ( 18) covalent geometry : bond 0.00240 (13163) covalent geometry : angle 0.51255 (17901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10437.46 seconds wall clock time: 179 minutes 54.22 seconds (10794.22 seconds total)