Starting phenix.real_space_refine on Thu Sep 18 01:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvq_47215/09_2025/9dvq_47215.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvq_47215/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dvq_47215/09_2025/9dvq_47215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvq_47215/09_2025/9dvq_47215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvq_47215/09_2025/9dvq_47215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvq_47215/09_2025/9dvq_47215.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.40, per 1000 atoms: 0.27 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: 1.23 Conformation dependent library (CDL) restraints added in 651.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.60 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: 2.80 Time building geometry restraints manager: 1.60 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (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 ARG 0.002 0.000 ARG A 343 TYR 0.017 0.001 TYR A 113 PHE 0.023 0.001 PHE G 227 TRP 0.012 0.001 TRP A 155 HIS 0.004 0.001 HIS B 698 Details of bonding type rmsd covalent geometry : bond 0.00469 (13163) covalent geometry : angle 0.60566 (17901) SS BOND : bond 0.07341 ( 9) SS BOND : angle 7.70005 ( 18) hydrogen bonds : bond 0.14480 ( 420) hydrogen bonds : angle 6.34264 ( 1179) link_NAG-ASN : bond 0.00232 ( 8) link_NAG-ASN : angle 2.61298 ( 24) *********************** 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 : 0.552 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: 0.7514 time to fit residues: 233.3347 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 : 0.506 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.083792 restraints weight = 18840.057| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.62 r_work: 0.2875 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13180 Z= 0.151 Angle : 0.569 7.728 17943 Z= 0.306 Chirality : 0.047 0.378 1897 Planarity : 0.004 0.037 2268 Dihedral : 5.636 54.333 1929 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.20 % Allowed : 18.05 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1554 helix: 0.41 (0.35), residues: 236 sheet: 0.64 (0.23), residues: 473 loop : -1.23 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.023 0.002 TYR B 87 PHE 0.023 0.001 PHE G 227 TRP 0.011 0.002 TRP A 155 HIS 0.005 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00369 (13163) covalent geometry : angle 0.55695 (17901) SS BOND : bond 0.00603 ( 9) SS BOND : angle 1.78495 ( 18) hydrogen bonds : bond 0.04916 ( 420) hydrogen bonds : angle 4.96226 ( 1179) link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 2.80887 ( 24) *********************** 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 302 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 272 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 146 LEU cc_start: 0.8564 (mt) cc_final: 0.8363 (mt) REVERT: A 158 VAL cc_start: 0.8733 (t) cc_final: 0.8529 (m) REVERT: A 332 CYS cc_start: 0.7418 (m) cc_final: 0.7032 (m) REVERT: A 350 PHE cc_start: 0.8760 (t80) cc_final: 0.8352 (t80) REVERT: A 446 GLU cc_start: 0.7995 (mp0) cc_final: 0.7748 (mp0) REVERT: A 483 GLN cc_start: 0.8236 (tp40) cc_final: 0.7801 (tp40) REVERT: A 679 ASN cc_start: 0.7848 (t0) cc_final: 0.7563 (t0) REVERT: B 66 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 95 MET cc_start: 0.8587 (mmm) cc_final: 0.8258 (mmm) REVERT: B 353 SER cc_start: 0.8438 (m) cc_final: 0.8223 (p) REVERT: B 458 TYR cc_start: 0.8301 (m-80) cc_final: 0.7671 (m-80) REVERT: B 483 GLN cc_start: 0.8273 (pt0) cc_final: 0.8019 (pt0) REVERT: B 493 GLU cc_start: 0.7484 (pm20) cc_final: 0.7272 (pm20) REVERT: B 502 GLN cc_start: 0.8623 (pt0) cc_final: 0.8415 (pt0) REVERT: B 573 ASP cc_start: 0.7734 (m-30) cc_final: 0.7434 (OUTLIER) REVERT: B 591 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8408 (mtpp) REVERT: B 687 GLU cc_start: 0.8078 (tp30) cc_final: 0.7763 (tp30) outliers start: 30 outliers final: 12 residues processed: 287 average time/residue: 0.7536 time to fit residues: 232.3965 Evaluate side-chains 269 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 439 VAL 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 178 ASP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 31 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 712 GLN B 74 ASN B 80 ASN B 405 GLN B 500 ASN B 679 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 = 0.3269 r_free = 0.3269 target = 0.100869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.084347 restraints weight = 18865.591| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.66 r_work: 0.2890 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1385 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= 0.117 Angle : 0.520 7.104 17943 Z= 0.283 Chirality : 0.045 0.338 1897 Planarity : 0.004 0.038 2268 Dihedral : 5.236 55.097 1919 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.42 % Allowed : 18.42 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1554 helix: 0.50 (0.35), residues: 236 sheet: 0.72 (0.23), residues: 480 loop : -1.21 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 93 TYR 0.017 0.001 TYR A 113 PHE 0.021 0.001 PHE G 227 TRP 0.011 0.001 TRP A 122 HIS 0.002 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00279 (13163) covalent geometry : angle 0.50993 (17901) SS BOND : bond 0.00509 ( 9) SS BOND : angle 1.50117 ( 18) hydrogen bonds : bond 0.04270 ( 420) hydrogen bonds : angle 4.74809 ( 1179) link_NAG-ASN : bond 0.00296 ( 8) link_NAG-ASN : angle 2.61784 ( 24) *********************** 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 302 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 269 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 332 CYS cc_start: 0.7433 (m) cc_final: 0.7025 (m) REVERT: A 350 PHE cc_start: 0.8761 (t80) cc_final: 0.8418 (t80) REVERT: A 446 GLU cc_start: 0.8005 (mp0) cc_final: 0.7756 (mp0) REVERT: A 483 GLN cc_start: 0.8245 (tp40) cc_final: 0.7841 (tp40) REVERT: B 66 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 95 MET cc_start: 0.8564 (mmm) cc_final: 0.8211 (mmm) REVERT: B 148 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8083 (ttm110) REVERT: B 359 TYR cc_start: 0.7958 (t80) cc_final: 0.7681 (t80) REVERT: B 458 TYR cc_start: 0.8284 (m-80) cc_final: 0.7725 (m-80) REVERT: B 483 GLN cc_start: 0.8262 (pt0) cc_final: 0.8020 (pt0) REVERT: B 573 ASP cc_start: 0.7704 (m-30) cc_final: 0.7402 (m-30) REVERT: B 687 GLU cc_start: 0.8077 (tp30) cc_final: 0.7759 (tp30) outliers start: 33 outliers final: 21 residues processed: 284 average time/residue: 0.7657 time to fit residues: 233.4466 Evaluate side-chains 287 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 SER 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 91 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 436 LYS 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 200 MET Chi-restraints excluded: chain G residue 232 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 139 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 500 ASN B 679 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 = 0.3237 r_free = 0.3237 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.082951 restraints weight = 18796.553| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.61 r_work: 0.2854 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 13180 Z= 0.238 Angle : 0.643 11.654 17943 Z= 0.345 Chirality : 0.050 0.381 1897 Planarity : 0.005 0.041 2268 Dihedral : 5.587 56.929 1919 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.15 % Allowed : 18.20 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1554 helix: 0.27 (0.34), residues: 236 sheet: 0.71 (0.23), residues: 473 loop : -1.32 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 93 TYR 0.025 0.002 TYR A 113 PHE 0.027 0.002 PHE G 227 TRP 0.014 0.002 TRP A 214 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00607 (13163) covalent geometry : angle 0.63175 (17901) SS BOND : bond 0.00559 ( 9) SS BOND : angle 1.58859 ( 18) hydrogen bonds : bond 0.05920 ( 420) hydrogen bonds : angle 4.97858 ( 1179) link_NAG-ASN : bond 0.00178 ( 8) link_NAG-ASN : angle 3.11379 ( 24) *********************** 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 314 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 332 CYS cc_start: 0.7369 (m) cc_final: 0.7013 (m) REVERT: A 350 PHE cc_start: 0.8721 (t80) cc_final: 0.8394 (t80) REVERT: A 404 THR cc_start: 0.8506 (t) cc_final: 0.8236 (p) REVERT: A 446 GLU cc_start: 0.8038 (mp0) cc_final: 0.7794 (mp0) REVERT: A 483 GLN cc_start: 0.8214 (tp40) cc_final: 0.7759 (tp40) REVERT: A 679 ASN cc_start: 0.7997 (t0) cc_final: 0.7640 (t0) REVERT: B 66 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 88 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8336 (t) REVERT: B 95 MET cc_start: 0.8568 (mmm) cc_final: 0.8288 (mmm) REVERT: B 139 GLU cc_start: 0.7365 (pm20) cc_final: 0.7067 (pt0) REVERT: B 402 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7432 (tpp-160) REVERT: B 458 TYR cc_start: 0.8297 (m-80) cc_final: 0.7806 (m-80) REVERT: B 483 GLN cc_start: 0.8245 (pt0) cc_final: 0.8034 (pt0) REVERT: B 573 ASP cc_start: 0.7823 (m-30) cc_final: 0.7530 (m-30) REVERT: B 617 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.6863 (mtt180) REVERT: B 687 GLU cc_start: 0.8009 (tp30) cc_final: 0.7720 (tp30) REVERT: G 166 SER cc_start: 0.8234 (t) cc_final: 0.7892 (m) outliers start: 43 outliers final: 26 residues processed: 290 average time/residue: 0.7675 time to fit residues: 239.1227 Evaluate side-chains 296 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 LEU 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 385 GLU Chi-restraints excluded: chain A residue 392 SER 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 162 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 362 ILE 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 512 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 500 ASN B 679 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.083800 restraints weight = 18690.718| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.61 r_work: 0.2874 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13180 Z= 0.163 Angle : 0.579 11.541 17943 Z= 0.312 Chirality : 0.047 0.358 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.472 56.375 1919 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.79 % Allowed : 18.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1554 helix: 0.33 (0.34), residues: 236 sheet: 0.72 (0.23), residues: 473 loop : -1.30 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 93 TYR 0.019 0.002 TYR A 113 PHE 0.025 0.001 PHE G 227 TRP 0.019 0.002 TRP B 327 HIS 0.002 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00404 (13163) covalent geometry : angle 0.56753 (17901) SS BOND : bond 0.00397 ( 9) SS BOND : angle 1.56594 ( 18) hydrogen bonds : bond 0.05039 ( 420) hydrogen bonds : angle 4.85743 ( 1179) link_NAG-ASN : bond 0.00225 ( 8) link_NAG-ASN : angle 2.92401 ( 24) *********************** 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 308 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 332 CYS cc_start: 0.7366 (m) cc_final: 0.6962 (m) REVERT: A 404 THR cc_start: 0.8464 (t) cc_final: 0.8194 (p) REVERT: A 446 GLU cc_start: 0.8023 (mp0) cc_final: 0.7779 (mp0) REVERT: A 483 GLN cc_start: 0.8218 (tp40) cc_final: 0.7763 (tp40) REVERT: B 66 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 88 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8347 (t) REVERT: B 95 MET cc_start: 0.8578 (mmm) cc_final: 0.8293 (mmm) REVERT: B 139 GLU cc_start: 0.7404 (pm20) cc_final: 0.7178 (pt0) REVERT: B 148 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8116 (ttm110) REVERT: B 458 TYR cc_start: 0.8294 (m-80) cc_final: 0.7792 (m-80) REVERT: B 483 GLN cc_start: 0.8224 (pt0) cc_final: 0.8011 (pt0) REVERT: B 573 ASP cc_start: 0.7792 (m-30) cc_final: 0.7492 (m-30) REVERT: B 617 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6827 (mtt180) REVERT: B 687 GLU cc_start: 0.8012 (tp30) cc_final: 0.7720 (tp30) outliers start: 38 outliers final: 23 residues processed: 288 average time/residue: 0.7762 time to fit residues: 239.8298 Evaluate side-chains 294 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 SER 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 178 ASP 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 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 506 GLU 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 111 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 74 ASN B 174 GLN B 500 ASN B 709 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.083822 restraints weight = 18529.527| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.60 r_work: 0.2882 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13180 Z= 0.146 Angle : 0.567 10.880 17943 Z= 0.305 Chirality : 0.046 0.357 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.374 56.164 1919 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.93 % Allowed : 18.93 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1554 helix: 0.39 (0.34), residues: 236 sheet: 0.75 (0.23), residues: 473 loop : -1.28 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.018 0.002 TYR A 113 PHE 0.025 0.001 PHE G 227 TRP 0.029 0.002 TRP B 327 HIS 0.002 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00358 (13163) covalent geometry : angle 0.55516 (17901) SS BOND : bond 0.00456 ( 9) SS BOND : angle 1.64781 ( 18) hydrogen bonds : bond 0.04741 ( 420) hydrogen bonds : angle 4.81524 ( 1179) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 2.83493 ( 24) *********************** 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 311 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 271 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 332 CYS cc_start: 0.7383 (m) cc_final: 0.6978 (m) REVERT: A 404 THR cc_start: 0.8480 (t) cc_final: 0.8229 (p) REVERT: A 446 GLU cc_start: 0.8025 (mp0) cc_final: 0.7781 (mp0) REVERT: A 483 GLN cc_start: 0.8214 (tp40) cc_final: 0.7763 (tp40) REVERT: B 66 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 88 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8353 (t) REVERT: B 95 MET cc_start: 0.8563 (mmm) cc_final: 0.8266 (mmm) REVERT: B 148 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8111 (ttm110) REVERT: B 458 TYR cc_start: 0.8293 (m-80) cc_final: 0.7785 (m-80) REVERT: B 483 GLN cc_start: 0.8213 (pt0) cc_final: 0.7998 (pt0) REVERT: B 573 ASP cc_start: 0.7769 (m-30) cc_final: 0.7466 (m-30) REVERT: B 617 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.6832 (mtt180) REVERT: B 687 GLU cc_start: 0.8016 (tp30) cc_final: 0.7656 (tp30) REVERT: G 166 SER cc_start: 0.7945 (t) cc_final: 0.7727 (t) outliers start: 40 outliers final: 23 residues processed: 292 average time/residue: 0.7879 time to fit residues: 246.4932 Evaluate side-chains 296 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 LEU 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 427 ILE Chi-restraints excluded: chain A residue 466 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 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 178 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 394 LYS 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 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 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 11 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 79 optimal weight: 0.0980 chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.100254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084051 restraints weight = 18632.230| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.60 r_work: 0.2885 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13180 Z= 0.145 Angle : 0.564 10.781 17943 Z= 0.304 Chirality : 0.046 0.357 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.363 56.760 1919 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.86 % Allowed : 19.74 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1554 helix: 0.15 (0.34), residues: 248 sheet: 0.73 (0.23), residues: 473 loop : -1.32 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.018 0.002 TYR A 113 PHE 0.024 0.001 PHE G 227 TRP 0.020 0.002 TRP B 327 HIS 0.002 0.001 HIS B 706 Details of bonding type rmsd covalent geometry : bond 0.00356 (13163) covalent geometry : angle 0.55280 (17901) SS BOND : bond 0.00449 ( 9) SS BOND : angle 1.85611 ( 18) hydrogen bonds : bond 0.04706 ( 420) hydrogen bonds : angle 4.78590 ( 1179) link_NAG-ASN : bond 0.00229 ( 8) link_NAG-ASN : angle 2.77405 ( 24) *********************** 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: 39 poor density : 272 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8667 (mp) REVERT: A 332 CYS cc_start: 0.7389 (m) cc_final: 0.6982 (m) REVERT: A 404 THR cc_start: 0.8480 (t) cc_final: 0.8231 (p) REVERT: A 446 GLU cc_start: 0.8048 (mp0) cc_final: 0.7804 (mp0) REVERT: A 483 GLN cc_start: 0.8232 (tp40) cc_final: 0.7775 (tp40) REVERT: B 66 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8282 (mt-10) REVERT: B 88 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (t) REVERT: B 95 MET cc_start: 0.8554 (mmm) cc_final: 0.8255 (mmm) REVERT: B 123 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7191 (ttt180) REVERT: B 351 PHE cc_start: 0.8563 (m-80) cc_final: 0.8313 (m-80) REVERT: B 402 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7391 (tpp-160) REVERT: B 458 TYR cc_start: 0.8294 (m-80) cc_final: 0.7814 (m-80) REVERT: B 483 GLN cc_start: 0.8222 (pt0) cc_final: 0.7989 (pt0) REVERT: B 573 ASP cc_start: 0.7770 (m-30) cc_final: 0.7466 (m-30) REVERT: B 617 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.6806 (mtt180) REVERT: G 166 SER cc_start: 0.7969 (t) cc_final: 0.7726 (t) outliers start: 39 outliers final: 25 residues processed: 291 average time/residue: 0.7802 time to fit residues: 243.5728 Evaluate side-chains 297 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 LEU 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 385 GLU Chi-restraints excluded: chain A residue 466 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 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 178 ASP Chi-restraints excluded: chain B residue 231 ILE 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 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 506 GLU Chi-restraints excluded: chain B residue 512 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 131 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7164 ------------------------------------------------------------------------------- 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 712 GLN A 721 GLN B 74 ASN B 500 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.084665 restraints weight = 18493.773| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.64 r_work: 0.2889 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1951 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= 0.126 Angle : 0.545 10.194 17943 Z= 0.295 Chirality : 0.046 0.354 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.276 57.370 1919 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.57 % Allowed : 19.74 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1554 helix: 0.21 (0.34), residues: 248 sheet: 0.68 (0.23), residues: 485 loop : -1.29 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 148 TYR 0.017 0.001 TYR A 113 PHE 0.023 0.001 PHE G 227 TRP 0.014 0.001 TRP B 327 HIS 0.002 0.001 HIS B 706 Details of bonding type rmsd covalent geometry : bond 0.00305 (13163) covalent geometry : angle 0.53446 (17901) SS BOND : bond 0.00419 ( 9) SS BOND : angle 1.63412 ( 18) hydrogen bonds : bond 0.04397 ( 420) hydrogen bonds : angle 4.73187 ( 1179) link_NAG-ASN : bond 0.00251 ( 8) link_NAG-ASN : angle 2.66402 ( 24) *********************** 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 302 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 CYS cc_start: 0.7383 (m) cc_final: 0.6980 (m) REVERT: A 404 THR cc_start: 0.8473 (t) cc_final: 0.8224 (p) REVERT: A 427 ILE cc_start: 0.8324 (mt) cc_final: 0.8093 (pt) REVERT: A 446 GLU cc_start: 0.8024 (mp0) cc_final: 0.7781 (mp0) REVERT: A 483 GLN cc_start: 0.8245 (tp40) cc_final: 0.7815 (tp40) REVERT: B 66 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 88 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8357 (t) REVERT: B 95 MET cc_start: 0.8547 (mmm) cc_final: 0.8247 (mmm) REVERT: B 123 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7190 (ttt180) REVERT: B 458 TYR cc_start: 0.8286 (m-80) cc_final: 0.7785 (m-80) REVERT: B 573 ASP cc_start: 0.7744 (m-30) cc_final: 0.7445 (m-30) REVERT: B 617 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6817 (mtt180) REVERT: G 166 SER cc_start: 0.7963 (t) cc_final: 0.7706 (t) outliers start: 35 outliers final: 23 residues processed: 282 average time/residue: 0.7879 time to fit residues: 238.0602 Evaluate side-chains 294 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR 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 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 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 178 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 436 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.101749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085221 restraints weight = 18727.593| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.66 r_work: 0.2900 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13180 Z= 0.109 Angle : 0.530 9.863 17943 Z= 0.285 Chirality : 0.045 0.346 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.120 56.584 1919 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.98 % Allowed : 20.47 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.21), residues: 1554 helix: 0.21 (0.33), residues: 252 sheet: 0.66 (0.23), residues: 489 loop : -1.28 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 148 TYR 0.016 0.001 TYR A 113 PHE 0.022 0.001 PHE G 227 TRP 0.015 0.001 TRP A 122 HIS 0.002 0.001 HIS B 750 Details of bonding type rmsd covalent geometry : bond 0.00257 (13163) covalent geometry : angle 0.52025 (17901) SS BOND : bond 0.00329 ( 9) SS BOND : angle 1.48554 ( 18) hydrogen bonds : bond 0.04062 ( 420) hydrogen bonds : angle 4.64396 ( 1179) link_NAG-ASN : bond 0.00273 ( 8) link_NAG-ASN : angle 2.55127 ( 24) *********************** 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 300 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 THR cc_start: 0.8467 (t) cc_final: 0.8226 (p) REVERT: A 427 ILE cc_start: 0.8312 (mt) cc_final: 0.8081 (pt) REVERT: A 446 GLU cc_start: 0.8016 (mp0) cc_final: 0.7772 (mp0) REVERT: A 483 GLN cc_start: 0.8247 (tp40) cc_final: 0.7819 (tp40) REVERT: B 66 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 88 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8365 (t) REVERT: B 95 MET cc_start: 0.8541 (mmm) cc_final: 0.8238 (mmm) REVERT: B 123 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7967 (ttm170) REVERT: B 271 TYR cc_start: 0.8325 (m-80) cc_final: 0.7786 (m-80) REVERT: B 351 PHE cc_start: 0.8540 (m-80) cc_final: 0.8295 (m-80) REVERT: B 402 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7351 (tpp-160) REVERT: B 458 TYR cc_start: 0.8283 (m-80) cc_final: 0.7812 (m-80) REVERT: B 573 ASP cc_start: 0.7739 (m-30) cc_final: 0.7433 (m-30) REVERT: B 617 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.6792 (mtt180) REVERT: G 166 SER cc_start: 0.7948 (t) cc_final: 0.7680 (t) outliers start: 27 outliers final: 18 residues processed: 286 average time/residue: 0.8011 time to fit residues: 245.4493 Evaluate side-chains 291 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR 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 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 123 ARG Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 231 ILE 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 436 LYS Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.101138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084874 restraints weight = 18691.677| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.61 r_work: 0.2899 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13180 Z= 0.120 Angle : 0.539 9.866 17943 Z= 0.290 Chirality : 0.045 0.344 1897 Planarity : 0.004 0.041 2268 Dihedral : 5.069 55.736 1919 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.05 % Allowed : 20.62 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1554 helix: 0.25 (0.33), residues: 252 sheet: 0.67 (0.23), residues: 489 loop : -1.29 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 148 TYR 0.017 0.001 TYR A 113 PHE 0.022 0.001 PHE G 227 TRP 0.020 0.001 TRP B 327 HIS 0.002 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00286 (13163) covalent geometry : angle 0.52955 (17901) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.48346 ( 18) hydrogen bonds : bond 0.04225 ( 420) hydrogen bonds : angle 4.64274 ( 1179) link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 2.54128 ( 24) ********************** 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 297 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 269 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 THR cc_start: 0.8476 (t) cc_final: 0.8247 (p) REVERT: A 427 ILE cc_start: 0.8308 (mt) cc_final: 0.8088 (pt) REVERT: A 446 GLU cc_start: 0.7998 (mp0) cc_final: 0.7762 (mp0) REVERT: A 483 GLN cc_start: 0.8254 (tp40) cc_final: 0.7816 (tp40) REVERT: B 66 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 88 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8357 (t) REVERT: B 95 MET cc_start: 0.8549 (mmm) cc_final: 0.8247 (mmm) REVERT: B 123 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7228 (ttt180) REVERT: B 402 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7352 (tpp-160) REVERT: B 458 TYR cc_start: 0.8273 (m-80) cc_final: 0.7815 (m-80) REVERT: B 573 ASP cc_start: 0.7732 (m-30) cc_final: 0.7434 (m-30) REVERT: B 617 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.6824 (mtt180) REVERT: B 679 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7809 (m110) REVERT: G 166 SER cc_start: 0.7956 (t) cc_final: 0.7679 (t) outliers start: 28 outliers final: 19 residues processed: 282 average time/residue: 0.8022 time to fit residues: 242.3993 Evaluate side-chains 295 residues out of total 1363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 88 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 123 ARG Chi-restraints excluded: chain B residue 178 ASP 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 436 LYS Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 643 CYS Chi-restraints excluded: chain B residue 679 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 151 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 496 ASN A 721 GLN B 500 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.082679 restraints weight = 18655.694| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.59 r_work: 0.2855 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 13180 Z= 0.262 Angle : 0.679 12.286 17943 Z= 0.361 Chirality : 0.051 0.376 1897 Planarity : 0.005 0.041 2268 Dihedral : 5.552 58.971 1919 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.35 % Allowed : 20.54 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.20), residues: 1554 helix: 0.22 (0.34), residues: 236 sheet: 0.73 (0.24), residues: 457 loop : -1.38 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 148 TYR 0.026 0.002 TYR A 113 PHE 0.028 0.002 PHE G 227 TRP 0.029 0.002 TRP B 327 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00668 (13163) covalent geometry : angle 0.66852 (17901) SS BOND : bond 0.00593 ( 9) SS BOND : angle 1.84613 ( 18) hydrogen bonds : bond 0.06145 ( 420) hydrogen bonds : angle 4.97658 ( 1179) link_NAG-ASN : bond 0.00202 ( 8) link_NAG-ASN : angle 2.92970 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5812.61 seconds wall clock time: 99 minutes 44.16 seconds (5984.16 seconds total)