Starting phenix.real_space_refine on Wed Jul 30 21:28:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.map" model { file = "/net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szf_40914/07_2025/8szf_40914.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.039 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 72 5.16 5 C 8305 2.51 5 N 2073 2.21 5 O 2351 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12813 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6243 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 31, 'TRANS': 767} Chain breaks: 3 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 6306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6306 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 31, 'TRANS': 769} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CA': 3, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' CA': 1, 'NAG': 1, 'PO4': 1, 'SPM': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.97, per 1000 atoms: 0.78 Number of scatterers: 12813 At special positions: 0 Unit cell: (103.256, 98.0501, 184.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 72 16.00 P 2 15.00 F 6 9.00 O 2351 8.00 N 2073 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1201 " - " ASN A 261 " " NAG A1202 " - " ASN A 468 " " NAG B1001 " - " ASN B 488 " " NAG B1002 " - " ASN B 468 " " NAG B1007 " - " ASN B 261 " " NAG C 1 " - " ASN A 541 " " NAG D 1 " - " ASN A 488 " " NAG E 1 " - " ASN B 541 " Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 2.2 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 14 sheets defined 48.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.608A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.646A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.720A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.616A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.663A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.075A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.561A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.580A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.926A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.584A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 4.173A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 667 removed outlier: 4.180A pdb=" N LEU A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 697 removed outlier: 4.883A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.977A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 removed outlier: 3.682A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.959A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.519A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 831 through 862 removed outlier: 4.284A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 862 " --> pdb=" O TYR A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.690A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.628A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.792A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.785A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.854A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.910A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.598A pdb=" N LYS B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 removed outlier: 3.600A pdb=" N SER B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.874A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 698 removed outlier: 3.850A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.637A pdb=" N PHE B 725 " --> pdb=" O LEU B 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 725' Processing helix chain 'B' and resid 726 through 746 Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.980A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 828 removed outlier: 3.526A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.776A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 876 removed outlier: 3.567A pdb=" N THR B 876 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.433A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.981A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.771A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.392A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 749 " --> pdb=" O HIS A 766 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.315A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.924A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.143A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N CYS B 765 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 764 " --> pdb=" O TYR B 751 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2047 1.31 - 1.44: 3738 1.44 - 1.57: 7254 1.57 - 1.70: 1 1.70 - 1.83: 86 Bond restraints: 13126 Sorted by residual: bond pdb=" CG YP4 A1208 " pdb=" CD1 YP4 A1208 " ideal model delta sigma weight residual 1.426 1.354 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CG YP4 B1006 " pdb=" CD1 YP4 B1006 " ideal model delta sigma weight residual 1.426 1.357 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O3 PO4 B1005 " pdb=" P PO4 B1005 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" O3 PO4 A1207 " pdb=" P PO4 A1207 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" O4 PO4 A1207 " pdb=" P PO4 A1207 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.58e+00 ... (remaining 13121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17352 2.01 - 4.01: 409 4.01 - 6.02: 52 6.02 - 8.02: 3 8.02 - 10.02: 4 Bond angle restraints: 17820 Sorted by residual: angle pdb=" N PRO B 641 " pdb=" CA PRO B 641 " pdb=" C PRO B 641 " ideal model delta sigma weight residual 113.53 123.39 -9.86 1.39e+00 5.18e-01 5.03e+01 angle pdb=" C CYS A 598 " pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sigma weight residual 109.38 117.80 -8.42 1.80e+00 3.09e-01 2.19e+01 angle pdb=" C PHE A 667 " pdb=" N PHE A 668 " pdb=" CA PHE A 668 " ideal model delta sigma weight residual 121.64 112.56 9.08 2.13e+00 2.20e-01 1.82e+01 angle pdb=" C THR B 640 " pdb=" N PRO B 641 " pdb=" CA PRO B 641 " ideal model delta sigma weight residual 119.05 123.00 -3.95 1.11e+00 8.12e-01 1.27e+01 angle pdb=" CA SER A 597 " pdb=" C SER A 597 " pdb=" O SER A 597 " ideal model delta sigma weight residual 121.06 117.03 4.03 1.16e+00 7.43e-01 1.21e+01 ... (remaining 17815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7140 17.33 - 34.66: 575 34.66 - 51.99: 122 51.99 - 69.32: 17 69.32 - 86.66: 8 Dihedral angle restraints: 7862 sinusoidal: 3206 harmonic: 4656 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 170.80 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 144.29 -51.29 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C CYS A 598 " pdb=" N CYS A 598 " pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " ideal model delta harmonic sigma weight residual -122.60 -137.04 14.44 0 2.50e+00 1.60e-01 3.34e+01 ... (remaining 7859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1895 0.101 - 0.202: 116 0.202 - 0.303: 5 0.303 - 0.404: 2 0.404 - 0.504: 1 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.00e+00 chirality pdb=" CA CYS A 598 " pdb=" N CYS A 598 " pdb=" C CYS A 598 " pdb=" CB CYS A 598 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CB THR B 640 " pdb=" CA THR B 640 " pdb=" OG1 THR B 640 " pdb=" CG2 THR B 640 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2016 not shown) Planarity restraints: 2247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 578 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C ASP A 578 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP A 578 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 579 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 648 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ARG A 648 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG A 648 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 649 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 861 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C LEU B 861 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU B 861 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE B 862 " 0.015 2.00e-02 2.50e+03 ... (remaining 2244 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3085 2.79 - 3.32: 11336 3.32 - 3.85: 19931 3.85 - 4.37: 23631 4.37 - 4.90: 41074 Nonbonded interactions: 99057 Sorted by model distance: nonbonded pdb=" OE1 GLU A 456 " pdb=" NE1 TRP A 458 " model vdw 2.268 3.120 nonbonded pdb=" O ALA A 168 " pdb=" N TRP A1203 " model vdw 2.294 3.120 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.314 3.120 nonbonded pdb=" OG1 THR B 470 " pdb=" OE1 GLN B 476 " model vdw 2.316 3.040 nonbonded pdb=" NH1 ARG A 551 " pdb=" O LYS A 552 " model vdw 2.325 3.120 ... (remaining 99052 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' and (resid 20 through 119 or (resid 120 through 121 and (name N or na \ me CA or name C or name O or name CB )) or resid 122 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 635 or (resid 636 and (name N or name CA o \ r name C or name O or name CB )) or resid 637 through 698 or (resid 699 through \ 701 and (name N or name CA or name C or name O or name CB )) or (resid 703 and ( \ name N or name CA or name C or name O or name CB )) or resid 722 through 862 or \ (resid 863 and (name N or name CA or name C or name O or name CB )) or resid 864 \ through 865 or (resid 866 through 867 and (name N or name CA or name C or name \ O or name CB )) or resid 868 through 871 or (resid 872 through 873 and (name N o \ r name CA or name C or name O or name CB )) or resid 874 or resid 1201 through 1 \ 203 or resid 1204)) selection = (chain 'B' and (resid 20 through 123 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 392 through 404 \ or (resid 405 and (name N or name CA or name C or name O or name CB )) or resid \ 406 through 480 or (resid 481 and (name N or name CA or name C or name O or nam \ e CB )) or resid 482 through 498 or (resid 499 through 500 and (name N or name C \ A or name C or name O or name CB )) or resid 501 through 592 or (resid 593 and ( \ name N or name CA or name C or name O or name CB )) or resid 594 through 601 or \ (resid 602 and (name N or name CA or name C or name O or name CB )) or resid 603 \ through 634 or (resid 635 through 636 and (name N or name CA or name C or name \ O or name CB )) or resid 637 or (resid 638 and (name N or name CA or name C or n \ ame O or name CB )) or resid 639 through 648 or (resid 649 and (name N or name C \ A or name C or name O or name CB )) or resid 650 through 670 or (resid 671 and ( \ name N or name CA or name C or name O or name CB )) or resid 672 through 699 or \ (resid 700 through 701 and (name N or name CA or name C or name O or name CB )) \ or resid 721 through 729 or (resid 730 and (name N or name CA or name C or name \ O or name CB )) or resid 731 through 758 or (resid 759 and (name N or name CA or \ name C or name O or name CB )) or resid 760 through 795 or (resid 796 and (name \ N or name CA or name C or name O or name CB )) or resid 797 through 802 or (res \ id 803 through 804 and (name N or name CA or name C or name O or name CB )) or r \ esid 805 through 853 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 868 or (resid 869 through 873 and (name N or na \ me CA or name C or name O or name CB )) or resid 874 or resid 1001 through 1003 \ or resid 1004)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 287.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.370 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 340.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.095 13155 Z= 0.274 Angle : 0.716 10.025 17889 Z= 0.407 Chirality : 0.052 0.504 2019 Planarity : 0.005 0.047 2239 Dihedral : 13.190 86.655 4796 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1584 helix: 1.35 (0.20), residues: 686 sheet: -0.93 (0.34), residues: 214 loop : -1.01 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 742 HIS 0.006 0.001 HIS A 463 PHE 0.038 0.002 PHE B 789 TYR 0.024 0.002 TYR B 744 ARG 0.006 0.000 ARG B 648 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 8) link_NAG-ASN : angle 3.10381 ( 24) link_BETA1-4 : bond 0.00742 ( 3) link_BETA1-4 : angle 1.28771 ( 9) hydrogen bonds : bond 0.17109 ( 573) hydrogen bonds : angle 5.39952 ( 1656) SS BOND : bond 0.00367 ( 18) SS BOND : angle 1.64186 ( 36) covalent geometry : bond 0.00504 (13126) covalent geometry : angle 0.70368 (17820) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.183 Fit side-chains revert: symmetry clash REVERT: A 536 GLU cc_start: 0.7080 (pp20) cc_final: 0.6860 (pp20) REVERT: B 647 ASN cc_start: 0.6701 (t0) cc_final: 0.6259 (m110) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.3577 time to fit residues: 221.3791 Evaluate side-chains 111 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 49 GLN A 118 ASN A 722 ASN B 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.102567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083483 restraints weight = 24819.111| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.01 r_work: 0.3128 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13155 Z= 0.141 Angle : 0.562 9.162 17889 Z= 0.303 Chirality : 0.043 0.167 2019 Planarity : 0.004 0.049 2239 Dihedral : 6.203 67.623 1971 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.19 % Allowed : 7.78 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1584 helix: 1.72 (0.19), residues: 691 sheet: -0.82 (0.35), residues: 216 loop : -0.98 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 818 HIS 0.003 0.001 HIS A 429 PHE 0.015 0.001 PHE B 634 TYR 0.016 0.002 TYR B 858 ARG 0.004 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 8) link_NAG-ASN : angle 2.11010 ( 24) link_BETA1-4 : bond 0.00198 ( 3) link_BETA1-4 : angle 1.35130 ( 9) hydrogen bonds : bond 0.06688 ( 573) hydrogen bonds : angle 4.32868 ( 1656) SS BOND : bond 0.00303 ( 18) SS BOND : angle 1.30795 ( 36) covalent geometry : bond 0.00299 (13126) covalent geometry : angle 0.55371 (17820) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.640 Fit side-chains REVERT: A 231 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 536 GLU cc_start: 0.7353 (pp20) cc_final: 0.6856 (pp20) REVERT: A 793 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7753 (mtpp) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 1.7711 time to fit residues: 251.7984 Evaluate side-chains 119 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 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 24 GLN A 309 GLN A 766 HIS B 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083649 restraints weight = 25224.374| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.24 r_work: 0.3133 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13155 Z= 0.119 Angle : 0.510 5.435 17889 Z= 0.273 Chirality : 0.042 0.156 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.736 66.429 1971 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.48 % Allowed : 8.97 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1584 helix: 1.92 (0.19), residues: 692 sheet: -0.90 (0.34), residues: 218 loop : -0.88 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 818 HIS 0.003 0.001 HIS A 429 PHE 0.011 0.001 PHE A 444 TYR 0.013 0.001 TYR B 421 ARG 0.002 0.000 ARG A 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 8) link_NAG-ASN : angle 1.94130 ( 24) link_BETA1-4 : bond 0.00318 ( 3) link_BETA1-4 : angle 1.36632 ( 9) hydrogen bonds : bond 0.05752 ( 573) hydrogen bonds : angle 4.06242 ( 1656) SS BOND : bond 0.00247 ( 18) SS BOND : angle 1.04457 ( 36) covalent geometry : bond 0.00247 (13126) covalent geometry : angle 0.50242 (17820) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.354 Fit side-chains REVERT: A 332 GLU cc_start: 0.8557 (mp0) cc_final: 0.8175 (mp0) REVERT: A 536 GLU cc_start: 0.7341 (pp20) cc_final: 0.6855 (pp20) REVERT: A 609 THR cc_start: 0.8297 (m) cc_final: 0.8018 (m) REVERT: A 793 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7792 (mtpp) REVERT: B 27 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: B 761 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8073 (mt) outliers start: 20 outliers final: 7 residues processed: 128 average time/residue: 1.0823 time to fit residues: 153.3391 Evaluate side-chains 120 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 857 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 3.9990 chunk 118 optimal weight: 0.0010 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 0.0060 chunk 149 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 463 HIS A 493 ASN B 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.104121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084698 restraints weight = 24932.791| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.25 r_work: 0.3157 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13155 Z= 0.105 Angle : 0.481 6.109 17889 Z= 0.257 Chirality : 0.041 0.153 2019 Planarity : 0.004 0.062 2239 Dihedral : 5.460 65.705 1971 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.41 % Allowed : 10.30 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1584 helix: 2.04 (0.19), residues: 694 sheet: -0.88 (0.35), residues: 218 loop : -0.80 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.004 0.001 HIS A 463 PHE 0.012 0.001 PHE A 619 TYR 0.018 0.001 TYR B 435 ARG 0.011 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 8) link_NAG-ASN : angle 1.75964 ( 24) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.25128 ( 9) hydrogen bonds : bond 0.05046 ( 573) hydrogen bonds : angle 3.90146 ( 1656) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.83877 ( 36) covalent geometry : bond 0.00210 (13126) covalent geometry : angle 0.47547 (17820) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.345 Fit side-chains REVERT: A 231 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 285 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7996 (ttp-110) REVERT: A 332 GLU cc_start: 0.8555 (mp0) cc_final: 0.8156 (mp0) REVERT: A 536 GLU cc_start: 0.7333 (pp20) cc_final: 0.6852 (pp20) REVERT: B 27 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: B 644 LYS cc_start: 0.7707 (mtpp) cc_final: 0.7477 (mttp) REVERT: B 761 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8143 (mt) outliers start: 19 outliers final: 7 residues processed: 133 average time/residue: 1.0849 time to fit residues: 159.7961 Evaluate side-chains 120 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 10 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 359 HIS A 493 ASN A 766 HIS B 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.099760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080151 restraints weight = 24935.835| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.27 r_work: 0.3059 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13155 Z= 0.252 Angle : 0.674 7.057 17889 Z= 0.359 Chirality : 0.048 0.208 2019 Planarity : 0.005 0.056 2239 Dihedral : 6.051 65.765 1971 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.15 % Allowed : 10.97 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1584 helix: 1.50 (0.19), residues: 700 sheet: -1.00 (0.34), residues: 224 loop : -0.91 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 818 HIS 0.006 0.002 HIS B 429 PHE 0.023 0.002 PHE A 444 TYR 0.022 0.003 TYR B 435 ARG 0.007 0.001 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 2.63335 ( 24) link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 1.92732 ( 9) hydrogen bonds : bond 0.07980 ( 573) hydrogen bonds : angle 4.30668 ( 1656) SS BOND : bond 0.00570 ( 18) SS BOND : angle 1.61696 ( 36) covalent geometry : bond 0.00612 (13126) covalent geometry : angle 0.66311 (17820) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.549 Fit side-chains REVERT: A 231 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: A 332 GLU cc_start: 0.8625 (mp0) cc_final: 0.8240 (mp0) REVERT: A 536 GLU cc_start: 0.7498 (pp20) cc_final: 0.6982 (pp20) REVERT: A 737 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6816 (t) REVERT: A 793 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7786 (ttpp) REVERT: B 27 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: B 761 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8244 (mt) outliers start: 29 outliers final: 13 residues processed: 138 average time/residue: 1.1159 time to fit residues: 170.5731 Evaluate side-chains 127 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 154 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 766 HIS B 24 GLN B 400 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.101473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081863 restraints weight = 25225.811| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.28 r_work: 0.3095 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13155 Z= 0.138 Angle : 0.543 6.994 17889 Z= 0.290 Chirality : 0.043 0.202 2019 Planarity : 0.004 0.048 2239 Dihedral : 5.762 64.999 1971 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.08 % Allowed : 12.23 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1584 helix: 1.68 (0.19), residues: 701 sheet: -1.06 (0.34), residues: 226 loop : -0.85 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.003 0.001 HIS B 429 PHE 0.014 0.001 PHE A 444 TYR 0.014 0.001 TYR A 421 ARG 0.006 0.000 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 8) link_NAG-ASN : angle 2.19051 ( 24) link_BETA1-4 : bond 0.00350 ( 3) link_BETA1-4 : angle 1.53831 ( 9) hydrogen bonds : bond 0.06254 ( 573) hydrogen bonds : angle 4.13131 ( 1656) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.09522 ( 36) covalent geometry : bond 0.00302 (13126) covalent geometry : angle 0.53508 (17820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.385 Fit side-chains REVERT: A 61 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7295 (mt) REVERT: A 231 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 332 GLU cc_start: 0.8640 (mp0) cc_final: 0.8238 (mp0) REVERT: A 536 GLU cc_start: 0.7442 (pp20) cc_final: 0.6923 (pp20) REVERT: A 737 VAL cc_start: 0.7056 (OUTLIER) cc_final: 0.6813 (t) REVERT: A 793 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7753 (ttpp) REVERT: B 27 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8255 (pt0) REVERT: B 481 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: B 761 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8247 (mt) outliers start: 28 outliers final: 10 residues processed: 129 average time/residue: 1.1859 time to fit residues: 169.6904 Evaluate side-chains 125 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 146 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 463 HIS B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081564 restraints weight = 24861.810| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.26 r_work: 0.3089 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13155 Z= 0.154 Angle : 0.563 8.780 17889 Z= 0.300 Chirality : 0.044 0.178 2019 Planarity : 0.004 0.048 2239 Dihedral : 5.727 64.157 1971 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.15 % Allowed : 12.08 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1584 helix: 1.71 (0.19), residues: 699 sheet: -1.08 (0.34), residues: 226 loop : -0.88 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 818 HIS 0.003 0.001 HIS A 463 PHE 0.016 0.002 PHE A 444 TYR 0.014 0.002 TYR A 421 ARG 0.007 0.000 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 8) link_NAG-ASN : angle 2.21504 ( 24) link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 1.56659 ( 9) hydrogen bonds : bond 0.06476 ( 573) hydrogen bonds : angle 4.12550 ( 1656) SS BOND : bond 0.00368 ( 18) SS BOND : angle 1.15614 ( 36) covalent geometry : bond 0.00350 (13126) covalent geometry : angle 0.55437 (17820) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.450 Fit side-chains REVERT: A 61 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7269 (mt) REVERT: A 231 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 332 GLU cc_start: 0.8628 (mp0) cc_final: 0.8226 (mp0) REVERT: A 536 GLU cc_start: 0.7449 (pp20) cc_final: 0.6930 (pp20) REVERT: A 737 VAL cc_start: 0.7054 (OUTLIER) cc_final: 0.6789 (t) REVERT: A 793 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7712 (ttpp) REVERT: B 27 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: B 481 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: B 726 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7217 (mt) REVERT: B 761 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8260 (mt) outliers start: 29 outliers final: 11 residues processed: 135 average time/residue: 1.2039 time to fit residues: 179.4988 Evaluate side-chains 132 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 726 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 78 optimal weight: 0.0170 chunk 137 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 131 optimal weight: 0.0370 chunk 73 optimal weight: 0.6980 chunk 117 optimal weight: 0.0270 chunk 110 optimal weight: 4.9990 chunk 21 optimal weight: 0.0030 overall best weight: 0.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 493 ASN B 24 GLN B 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085244 restraints weight = 25267.896| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.30 r_work: 0.3169 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13155 Z= 0.099 Angle : 0.470 8.304 17889 Z= 0.249 Chirality : 0.040 0.171 2019 Planarity : 0.004 0.047 2239 Dihedral : 5.221 62.932 1971 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.48 % Allowed : 13.27 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1584 helix: 1.99 (0.19), residues: 696 sheet: -0.95 (0.35), residues: 218 loop : -0.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 299 HIS 0.001 0.000 HIS B 766 PHE 0.012 0.001 PHE B 539 TYR 0.018 0.001 TYR B 435 ARG 0.007 0.000 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 1.76035 ( 24) link_BETA1-4 : bond 0.00366 ( 3) link_BETA1-4 : angle 1.19865 ( 9) hydrogen bonds : bond 0.04368 ( 573) hydrogen bonds : angle 3.83333 ( 1656) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.91599 ( 36) covalent geometry : bond 0.00192 (13126) covalent geometry : angle 0.46364 (17820) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 332 GLU cc_start: 0.8600 (mp0) cc_final: 0.8180 (mp0) REVERT: A 359 HIS cc_start: 0.7707 (t-90) cc_final: 0.7155 (t-90) REVERT: A 536 GLU cc_start: 0.7308 (pp20) cc_final: 0.6810 (pp20) REVERT: A 793 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7378 (tmtt) REVERT: B 27 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8231 (pt0) REVERT: B 74 MET cc_start: 0.8617 (ttt) cc_final: 0.8401 (ttt) REVERT: B 761 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 853 PHE cc_start: 0.8021 (m-80) cc_final: 0.7683 (m-80) outliers start: 20 outliers final: 6 residues processed: 124 average time/residue: 1.1146 time to fit residues: 152.9495 Evaluate side-chains 115 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 493 ASN B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082189 restraints weight = 24972.682| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.26 r_work: 0.3099 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13155 Z= 0.154 Angle : 0.556 11.815 17889 Z= 0.295 Chirality : 0.043 0.169 2019 Planarity : 0.004 0.048 2239 Dihedral : 5.498 62.758 1971 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.26 % Allowed : 13.57 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1584 helix: 1.88 (0.19), residues: 699 sheet: -0.98 (0.34), residues: 226 loop : -0.77 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.015 0.002 PHE A 444 TYR 0.021 0.002 TYR B 435 ARG 0.008 0.001 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 8) link_NAG-ASN : angle 2.04509 ( 24) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 1.51005 ( 9) hydrogen bonds : bond 0.06126 ( 573) hydrogen bonds : angle 4.01977 ( 1656) SS BOND : bond 0.00329 ( 18) SS BOND : angle 1.17559 ( 36) covalent geometry : bond 0.00355 (13126) covalent geometry : angle 0.54802 (17820) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 61 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7178 (mt) REVERT: A 332 GLU cc_start: 0.8622 (mp0) cc_final: 0.8223 (mp0) REVERT: A 359 HIS cc_start: 0.7787 (t-90) cc_final: 0.7247 (t-90) REVERT: A 536 GLU cc_start: 0.7465 (pp20) cc_final: 0.6941 (pp20) REVERT: A 793 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7394 (tmtt) REVERT: B 27 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: B 761 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8269 (mt) REVERT: B 853 PHE cc_start: 0.8130 (m-80) cc_final: 0.7832 (m-80) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 1.2244 time to fit residues: 166.8367 Evaluate side-chains 119 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.0070 overall best weight: 0.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.102903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083372 restraints weight = 24947.532| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.23 r_work: 0.3129 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13155 Z= 0.113 Angle : 0.509 12.862 17889 Z= 0.269 Chirality : 0.042 0.176 2019 Planarity : 0.004 0.047 2239 Dihedral : 5.338 62.195 1971 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.11 % Allowed : 13.86 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1584 helix: 2.00 (0.19), residues: 690 sheet: -0.98 (0.34), residues: 226 loop : -0.75 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 299 HIS 0.002 0.001 HIS B 463 PHE 0.012 0.001 PHE B 853 TYR 0.024 0.001 TYR B 435 ARG 0.008 0.000 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 1.90319 ( 24) link_BETA1-4 : bond 0.00343 ( 3) link_BETA1-4 : angle 1.33057 ( 9) hydrogen bonds : bond 0.05234 ( 573) hydrogen bonds : angle 3.93461 ( 1656) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.91634 ( 36) covalent geometry : bond 0.00238 (13126) covalent geometry : angle 0.50215 (17820) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 332 GLU cc_start: 0.8624 (mp0) cc_final: 0.8220 (mp0) REVERT: A 359 HIS cc_start: 0.7705 (t-90) cc_final: 0.7178 (t-90) REVERT: A 536 GLU cc_start: 0.7358 (pp20) cc_final: 0.6871 (pp20) REVERT: A 737 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6866 (t) REVERT: A 793 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7349 (tmtt) REVERT: B 27 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: B 761 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 853 PHE cc_start: 0.8091 (m-80) cc_final: 0.7753 (m-80) outliers start: 15 outliers final: 7 residues processed: 121 average time/residue: 1.1095 time to fit residues: 148.6829 Evaluate side-chains 118 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 493 ASN B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083039 restraints weight = 25059.418| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.22 r_work: 0.3123 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13155 Z= 0.121 Angle : 0.520 13.622 17889 Z= 0.275 Chirality : 0.042 0.202 2019 Planarity : 0.004 0.047 2239 Dihedral : 5.332 61.527 1971 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.19 % Allowed : 13.79 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1584 helix: 1.94 (0.19), residues: 696 sheet: -0.96 (0.34), residues: 226 loop : -0.74 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 818 HIS 0.002 0.001 HIS B 429 PHE 0.013 0.001 PHE B 853 TYR 0.024 0.001 TYR B 435 ARG 0.008 0.000 ARG B 795 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 8) link_NAG-ASN : angle 1.90251 ( 24) link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 1.34544 ( 9) hydrogen bonds : bond 0.05425 ( 573) hydrogen bonds : angle 3.94488 ( 1656) SS BOND : bond 0.00250 ( 18) SS BOND : angle 0.95811 ( 36) covalent geometry : bond 0.00262 (13126) covalent geometry : angle 0.51326 (17820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10450.13 seconds wall clock time: 185 minutes 41.38 seconds (11141.38 seconds total)