Starting phenix.real_space_refine on Sun Aug 24 07:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szh_40916/08_2025/8szh_40916.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.051 sd= 0.156 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 4 5.49 5 S 108 5.16 5 C 11657 2.51 5 N 2968 2.21 5 O 3315 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18062 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6579 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 802} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6385 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 3 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1770 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2505 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 84 Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 408 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" 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: "G" 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: "H" 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: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 144 Unusual residues: {' CA': 2, 'NAG': 1, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 187 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1408 "'] Classifications: {'peptide': 1, 'undetermined': 10, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.09, per 1000 atoms: 0.23 Number of scatterers: 18062 At special positions: 0 Unit cell: (91.9762, 114.536, 253.368, 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 108 16.00 P 4 15.00 F 6 9.00 O 3315 8.00 N 2968 7.00 C 11657 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=2.03 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=2.03 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 903 " - " ASN A 468 " " NAG B1404 " - " ASN B 468 " " NAG B1405 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 661.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 42.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 64 through 83 removed outlier: 3.704A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.526A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.512A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.722A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.632A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.625A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.026A 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: 3.592A 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: 3.581A pdb=" N ASN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.638A 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 removed outlier: 4.248A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.824A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 669 removed outlier: 3.627A pdb=" N PHE A 668 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 669' Processing helix chain 'A' and resid 675 through 707 removed outlier: 5.576A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.909A pdb=" N CYS A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 722 through 746 removed outlier: 3.807A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 removed outlier: 3.964A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 788 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.957A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 813 " --> pdb=" O PHE A 809 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.915A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 877 removed outlier: 4.001A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 874 " --> pdb=" O GLU A 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 83 removed outlier: 3.683A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.846A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.680A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.572A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.790A 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 233 removed outlier: 3.962A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.563A pdb=" N VAL B 258 " --> pdb=" O HIS B 254 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) 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 416 through 436 removed outlier: 3.606A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.991A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.517A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) 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 removed outlier: 3.820A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.679A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.935A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 669 removed outlier: 3.523A pdb=" N PHE B 668 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 669' Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.972A pdb=" N ALA B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.217A pdb=" N LEU B 703 " --> pdb=" O THR B 699 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 704' Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.993A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.939A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 775 " --> pdb=" O MET B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 3.963A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 861 removed outlier: 3.608A pdb=" N ILE B 839 " --> pdb=" O ALA B 835 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 840 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 858 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 31 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 3.587A pdb=" N LYS C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 removed outlier: 4.134A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 228 through 231' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.563A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.769A pdb=" N PHE C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.945A pdb=" N ALA D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N CYS D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.780A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 8 through 24 removed outlier: 3.663A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.548A pdb=" N ALA E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.512A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.870A 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: 8.095A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.550A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 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: 6.370A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.238A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.055A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.490A 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 553 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: 6.204A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 186 through 190 removed outlier: 3.567A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 51 removed outlier: 3.630A pdb=" N ARG D 46 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 317 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 58 through 61 removed outlier: 6.814A pdb=" N ALA D 73 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.618A pdb=" N VAL D 112 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 124 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.158A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.731A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP D 212 " --> pdb=" O CYS D 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS D 218 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.754A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.650A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2097 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: 3.23 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2908 1.32 - 1.45: 5213 1.45 - 1.58: 10195 1.58 - 1.71: 18 1.71 - 1.84: 136 Bond restraints: 18470 Sorted by residual: bond pdb=" C31 PCW B1403 " pdb=" O2 PCW B1403 " ideal model delta sigma weight residual 1.333 1.488 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" C31 PCW A 902 " pdb=" O2 PCW A 902 " ideal model delta sigma weight residual 1.333 1.484 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C31 PCW B1403 " pdb=" C32 PCW B1403 " ideal model delta sigma weight residual 1.502 1.604 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C31 PCW A 902 " pdb=" C32 PCW A 902 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 PCW B1403 " pdb=" C17 PCW B1403 " ideal model delta sigma weight residual 1.523 1.622 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 18465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 24959 5.04 - 10.08: 56 10.08 - 15.12: 7 15.12 - 20.16: 3 20.16 - 25.20: 2 Bond angle restraints: 25027 Sorted by residual: angle pdb=" N ARG A 866 " pdb=" CA ARG A 866 " pdb=" C ARG A 866 " ideal model delta sigma weight residual 113.23 95.26 17.97 1.22e+00 6.72e-01 2.17e+02 angle pdb=" N ILE A 869 " pdb=" CA ILE A 869 " pdb=" C ILE A 869 " ideal model delta sigma weight residual 112.83 104.47 8.36 9.90e-01 1.02e+00 7.13e+01 angle pdb=" C18 PCW B1403 " pdb=" C19 PCW B1403 " pdb=" C20 PCW B1403 " ideal model delta sigma weight residual 127.82 153.02 -25.20 3.00e+00 1.11e-01 7.05e+01 angle pdb=" C18 PCW A 902 " pdb=" C19 PCW A 902 " pdb=" C20 PCW A 902 " ideal model delta sigma weight residual 127.82 152.59 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" CA PHE A 862 " pdb=" C PHE A 862 " pdb=" O PHE A 862 " ideal model delta sigma weight residual 121.78 111.37 10.41 1.28e+00 6.10e-01 6.62e+01 ... (remaining 25022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 10156 20.04 - 40.08: 794 40.08 - 60.11: 112 60.11 - 80.15: 24 80.15 - 100.19: 14 Dihedral angle restraints: 11100 sinusoidal: 4505 harmonic: 6595 Sorted by residual: 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 -86.00 -172.13 86.13 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 171.14 -78.14 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual -86.00 -41.20 -44.80 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 11097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2823 1.032 - 2.064: 0 2.064 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.159: 1 Chirality restraints: 2824 Sorted by residual: chirality pdb=" C2 PCW A 902 " pdb=" C1 PCW A 902 " pdb=" C3 PCW A 902 " pdb=" O2 PCW A 902 " both_signs ideal model delta sigma weight residual False -2.32 2.84 -5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" C2 PCW B1403 " pdb=" C1 PCW B1403 " pdb=" C3 PCW B1403 " pdb=" O2 PCW B1403 " both_signs ideal model delta sigma weight residual False -2.32 -2.81 0.49 2.00e-01 2.50e+01 6.02e+00 ... (remaining 2821 not shown) Planarity restraints: 3148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.198 2.00e-02 2.50e+03 1.63e-01 3.32e+02 pdb=" C7 NAG H 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.063 2.00e-02 2.50e+03 6.88e-02 5.92e+01 pdb=" CG ASN B 541 " 0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 541 " -0.031 2.00e-02 2.50e+03 6.44e-02 4.15e+01 pdb=" CG ASN B 541 " 0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN B 541 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN B 541 " -0.035 2.00e-02 2.50e+03 ... (remaining 3145 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1158 2.74 - 3.28: 16843 3.28 - 3.82: 27590 3.82 - 4.36: 33265 4.36 - 4.90: 59263 Nonbonded interactions: 138119 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.208 3.040 nonbonded pdb=" O PHE B 668 " pdb=" OG SER B 834 " model vdw 2.220 3.040 nonbonded pdb=" O LEU B 87 " pdb=" NE2 GLN B 432 " model vdw 2.227 3.120 nonbonded pdb=" OE1 GLN B 253 " pdb=" NH2 ARG B 286 " model vdw 2.250 3.120 ... (remaining 138114 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 131 or (resid 132 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 516 or (resid 517 and (name N or name CA or name C or name O or name CB )) \ or resid 518 through 586 or (resid 587 and (name N or name CA or name C or name \ O or name CB )) or resid 588 through 700 or (resid 701 and (name N or name CA o \ r name C or name O or name CB )) or resid 702 or (resid 703 and (name N or name \ CA or name C or name O or name CB )) or resid 704 through 706 or (resid 707 thro \ ugh 709 and (name N or name CA or name C or name O or name CB )) or resid 722 th \ rough 798 or (resid 799 and (name N or name CA or name C or name O or name CB )) \ or resid 800 through 861 or (resid 862 through 863 and (name N or name CA or na \ me C or name O or name CB )) or resid 864 through 865 or (resid 866 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 87 \ 0 or (resid 871 through 873 and (name N or name CA or name C or name O or name C \ B )) or resid 874 through 876 or resid 903 through 909)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 124 or (resid 125 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 131 through 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 361 or (resid 3 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 392 through \ 498 or (resid 499 through 500 and (name N or name CA or name C or name O or nam \ e CB )) or resid 501 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 867 or (resid 868 and (name N or na \ me CA or name C or name O or name CB )) or resid 869 through 876 or resid 1405 t \ hrough 1411)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.480 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.006 0.155 18497 Z= 0.313 Angle : 0.792 25.195 25090 Z= 0.442 Chirality : 0.110 5.159 2824 Planarity : 0.005 0.163 3142 Dihedral : 14.616 100.191 6776 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.18), residues: 2243 helix: 0.97 (0.18), residues: 882 sheet: -0.52 (0.27), residues: 379 loop : -1.16 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 886 TYR 0.042 0.002 TYR C 354 PHE 0.045 0.001 PHE B 612 TRP 0.027 0.001 TRP A 719 HIS 0.006 0.001 HIS A 715 Details of bonding type rmsd covalent geometry : bond 0.00577 (18470) covalent geometry : angle 0.78035 (25027) SS BOND : bond 0.00151 ( 18) SS BOND : angle 0.87724 ( 36) hydrogen bonds : bond 0.18210 ( 731) hydrogen bonds : angle 5.87086 ( 2097) link_BETA1-4 : bond 0.00415 ( 3) link_BETA1-4 : angle 2.57737 ( 9) link_NAG-ASN : bond 0.00459 ( 6) link_NAG-ASN : angle 4.66294 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7601 (mt-10) REVERT: B 336 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8224 (mptt) REVERT: B 558 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7617 (mp0) REVERT: B 609 THR cc_start: 0.8789 (m) cc_final: 0.8389 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1536 time to fit residues: 57.4694 Evaluate side-chains 196 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN B 117 GLN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071166 restraints weight = 37155.315| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.03 r_work: 0.2939 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18497 Z= 0.243 Angle : 0.652 6.845 25090 Z= 0.347 Chirality : 0.048 0.276 2824 Planarity : 0.005 0.050 3142 Dihedral : 8.991 91.664 2833 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.28 % Allowed : 8.01 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.17), residues: 2243 helix: 0.87 (0.18), residues: 895 sheet: -0.67 (0.27), residues: 373 loop : -1.31 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.018 0.002 TYR D 105 PHE 0.021 0.002 PHE A 634 TRP 0.020 0.002 TRP A 719 HIS 0.008 0.002 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00592 (18470) covalent geometry : angle 0.64522 (25027) SS BOND : bond 0.00336 ( 18) SS BOND : angle 1.47349 ( 36) hydrogen bonds : bond 0.07275 ( 731) hydrogen bonds : angle 4.66572 ( 2097) link_BETA1-4 : bond 0.00653 ( 3) link_BETA1-4 : angle 1.51602 ( 9) link_NAG-ASN : bond 0.00474 ( 6) link_NAG-ASN : angle 2.82507 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7569 (mt-10) REVERT: A 286 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7721 (mtt180) REVERT: A 789 PHE cc_start: 0.8203 (t80) cc_final: 0.7964 (t80) REVERT: B 558 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7648 (mp0) REVERT: B 609 THR cc_start: 0.8858 (m) cc_final: 0.8378 (p) outliers start: 24 outliers final: 16 residues processed: 211 average time/residue: 0.1349 time to fit residues: 41.9589 Evaluate side-chains 205 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 51 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072620 restraints weight = 37223.126| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.04 r_work: 0.2973 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18497 Z= 0.139 Angle : 0.525 6.598 25090 Z= 0.283 Chirality : 0.043 0.175 2824 Planarity : 0.004 0.049 3142 Dihedral : 8.436 90.327 2833 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.44 % Allowed : 10.30 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2243 helix: 1.15 (0.18), residues: 896 sheet: -0.62 (0.27), residues: 375 loop : -1.30 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.014 0.001 TYR A 421 PHE 0.015 0.001 PHE B 814 TRP 0.015 0.002 TRP A 719 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00316 (18470) covalent geometry : angle 0.51999 (25027) SS BOND : bond 0.00435 ( 18) SS BOND : angle 1.14793 ( 36) hydrogen bonds : bond 0.05683 ( 731) hydrogen bonds : angle 4.32252 ( 2097) link_BETA1-4 : bond 0.00333 ( 3) link_BETA1-4 : angle 1.36040 ( 9) link_NAG-ASN : bond 0.00282 ( 6) link_NAG-ASN : angle 2.23285 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8244 (t80) cc_final: 0.7991 (t80) REVERT: B 558 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7635 (mp0) REVERT: B 609 THR cc_start: 0.8885 (m) cc_final: 0.8387 (p) REVERT: B 753 ASN cc_start: 0.8049 (t0) cc_final: 0.7601 (t0) REVERT: D 229 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8223 (mt) REVERT: D 234 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8368 (m-10) outliers start: 27 outliers final: 16 residues processed: 213 average time/residue: 0.1474 time to fit residues: 46.1842 Evaluate side-chains 203 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 15 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 81 optimal weight: 0.0670 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073122 restraints weight = 37224.805| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.04 r_work: 0.2984 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18497 Z= 0.125 Angle : 0.512 9.341 25090 Z= 0.273 Chirality : 0.042 0.171 2824 Planarity : 0.004 0.048 3142 Dihedral : 8.087 87.729 2833 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.87 % Allowed : 11.80 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.18), residues: 2243 helix: 1.30 (0.18), residues: 892 sheet: -0.58 (0.27), residues: 374 loop : -1.28 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.016 0.001 TYR C 230 PHE 0.016 0.001 PHE B 814 TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00286 (18470) covalent geometry : angle 0.50767 (25027) SS BOND : bond 0.00297 ( 18) SS BOND : angle 0.97357 ( 36) hydrogen bonds : bond 0.05144 ( 731) hydrogen bonds : angle 4.13794 ( 2097) link_BETA1-4 : bond 0.00295 ( 3) link_BETA1-4 : angle 1.27013 ( 9) link_NAG-ASN : bond 0.00260 ( 6) link_NAG-ASN : angle 2.01412 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8253 (t80) cc_final: 0.7996 (t80) REVERT: B 336 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8381 (mptt) REVERT: B 558 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 609 THR cc_start: 0.8888 (m) cc_final: 0.8405 (p) REVERT: B 753 ASN cc_start: 0.8021 (t0) cc_final: 0.6867 (t0) REVERT: D 229 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8226 (mt) REVERT: D 234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8256 (m-80) outliers start: 35 outliers final: 23 residues processed: 215 average time/residue: 0.1470 time to fit residues: 46.7296 Evaluate side-chains 213 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073196 restraints weight = 36999.609| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.02 r_work: 0.2985 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18497 Z= 0.124 Angle : 0.499 6.706 25090 Z= 0.268 Chirality : 0.042 0.171 2824 Planarity : 0.004 0.048 3142 Dihedral : 7.935 86.700 2833 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.71 % Allowed : 12.76 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.18), residues: 2243 helix: 1.42 (0.18), residues: 890 sheet: -0.61 (0.27), residues: 374 loop : -1.26 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.015 0.001 TYR C 230 PHE 0.016 0.001 PHE B 814 TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00285 (18470) covalent geometry : angle 0.49512 (25027) SS BOND : bond 0.00203 ( 18) SS BOND : angle 1.03502 ( 36) hydrogen bonds : bond 0.05035 ( 731) hydrogen bonds : angle 4.08629 ( 2097) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 1.29981 ( 9) link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 1.98594 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8365 (mptt) REVERT: B 558 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7619 (mp0) REVERT: B 609 THR cc_start: 0.8902 (m) cc_final: 0.8419 (p) REVERT: B 697 VAL cc_start: 0.7611 (t) cc_final: 0.7307 (t) REVERT: D 229 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8231 (mt) outliers start: 32 outliers final: 23 residues processed: 216 average time/residue: 0.1554 time to fit residues: 50.0860 Evaluate side-chains 213 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 183 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 192 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 chunk 139 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 753 ASN C 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074226 restraints weight = 36845.684| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.02 r_work: 0.3011 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18497 Z= 0.097 Angle : 0.466 6.287 25090 Z= 0.250 Chirality : 0.041 0.158 2824 Planarity : 0.004 0.051 3142 Dihedral : 7.652 85.007 2833 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.55 % Allowed : 13.45 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2243 helix: 1.59 (0.18), residues: 891 sheet: -0.59 (0.27), residues: 376 loop : -1.19 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.015 0.001 TYR B 751 PHE 0.022 0.001 PHE D 235 TRP 0.013 0.001 TRP B 818 HIS 0.002 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00207 (18470) covalent geometry : angle 0.46199 (25027) SS BOND : bond 0.00161 ( 18) SS BOND : angle 0.83785 ( 36) hydrogen bonds : bond 0.04362 ( 731) hydrogen bonds : angle 3.93642 ( 2097) link_BETA1-4 : bond 0.00317 ( 3) link_BETA1-4 : angle 1.22756 ( 9) link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 1.78946 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 789 PHE cc_start: 0.8292 (t80) cc_final: 0.7966 (t80) REVERT: B 336 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8354 (mptt) REVERT: B 558 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7624 (mp0) REVERT: B 609 THR cc_start: 0.8896 (m) cc_final: 0.8415 (p) REVERT: B 876 THR cc_start: 0.5233 (OUTLIER) cc_final: 0.4858 (m) REVERT: C 291 THR cc_start: 0.8067 (t) cc_final: 0.7857 (t) outliers start: 29 outliers final: 20 residues processed: 213 average time/residue: 0.1458 time to fit residues: 45.8745 Evaluate side-chains 209 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 116 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 164 optimal weight: 0.0980 chunk 196 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 8 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073200 restraints weight = 37105.487| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.99 r_work: 0.2987 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18497 Z= 0.132 Angle : 0.500 5.897 25090 Z= 0.268 Chirality : 0.042 0.176 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.639 84.942 2833 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.76 % Allowed : 14.04 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2243 helix: 1.47 (0.18), residues: 900 sheet: -0.63 (0.27), residues: 373 loop : -1.19 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.014 0.001 TYR A 421 PHE 0.024 0.001 PHE D 235 TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00308 (18470) covalent geometry : angle 0.49598 (25027) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.96125 ( 36) hydrogen bonds : bond 0.05025 ( 731) hydrogen bonds : angle 3.98890 ( 2097) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.31260 ( 9) link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.96751 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: B 336 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8373 (mptt) REVERT: B 558 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7651 (mp0) REVERT: B 609 THR cc_start: 0.8910 (m) cc_final: 0.8435 (p) REVERT: B 697 VAL cc_start: 0.7695 (t) cc_final: 0.7326 (t) REVERT: B 876 THR cc_start: 0.5255 (OUTLIER) cc_final: 0.4882 (m) REVERT: C 291 THR cc_start: 0.8057 (t) cc_final: 0.7856 (t) REVERT: D 229 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8380 (mt) REVERT: D 235 PHE cc_start: 0.8065 (t80) cc_final: 0.7593 (t80) outliers start: 33 outliers final: 26 residues processed: 205 average time/residue: 0.1639 time to fit residues: 49.7733 Evaluate side-chains 217 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.073059 restraints weight = 37084.746| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.03 r_work: 0.2982 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18497 Z= 0.132 Angle : 0.506 8.067 25090 Z= 0.271 Chirality : 0.042 0.175 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.600 84.961 2833 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.71 % Allowed : 14.42 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2243 helix: 1.47 (0.18), residues: 900 sheet: -0.66 (0.27), residues: 371 loop : -1.22 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.018 0.001 TYR B 751 PHE 0.022 0.001 PHE D 235 TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00310 (18470) covalent geometry : angle 0.50135 (25027) SS BOND : bond 0.00231 ( 18) SS BOND : angle 1.07606 ( 36) hydrogen bonds : bond 0.05037 ( 731) hydrogen bonds : angle 3.99109 ( 2097) link_BETA1-4 : bond 0.00278 ( 3) link_BETA1-4 : angle 1.32995 ( 9) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 1.97650 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7408 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 336 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8370 (mptt) REVERT: B 558 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7630 (mp0) REVERT: B 609 THR cc_start: 0.8910 (m) cc_final: 0.8436 (p) REVERT: B 697 VAL cc_start: 0.7645 (t) cc_final: 0.7279 (t) REVERT: B 876 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.4872 (m) REVERT: D 17 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7386 (tt0) REVERT: D 229 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8210 (mt) outliers start: 32 outliers final: 25 residues processed: 207 average time/residue: 0.1505 time to fit residues: 46.1783 Evaluate side-chains 218 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 147 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 44 GLN D 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.072705 restraints weight = 36998.414| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.02 r_work: 0.2974 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18497 Z= 0.147 Angle : 0.519 6.645 25090 Z= 0.278 Chirality : 0.043 0.179 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.612 85.212 2833 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.92 % Allowed : 14.36 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.18), residues: 2243 helix: 1.44 (0.18), residues: 898 sheet: -0.66 (0.28), residues: 364 loop : -1.21 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 54 TYR 0.020 0.001 TYR B 751 PHE 0.025 0.001 PHE D 235 TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00349 (18470) covalent geometry : angle 0.51466 (25027) SS BOND : bond 0.00247 ( 18) SS BOND : angle 1.07275 ( 36) hydrogen bonds : bond 0.05262 ( 731) hydrogen bonds : angle 4.03484 ( 2097) link_BETA1-4 : bond 0.00291 ( 3) link_BETA1-4 : angle 1.35894 ( 9) link_NAG-ASN : bond 0.00268 ( 6) link_NAG-ASN : angle 2.03953 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7418 (tm-30) cc_final: 0.7118 (tm-30) REVERT: B 336 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8376 (mptt) REVERT: B 558 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7637 (mp0) REVERT: B 609 THR cc_start: 0.8913 (m) cc_final: 0.8440 (p) REVERT: B 697 VAL cc_start: 0.7629 (t) cc_final: 0.7288 (t) REVERT: B 876 THR cc_start: 0.5231 (OUTLIER) cc_final: 0.4871 (m) REVERT: D 17 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7354 (tt0) REVERT: D 229 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8263 (mt) outliers start: 36 outliers final: 33 residues processed: 213 average time/residue: 0.1524 time to fit residues: 48.4163 Evaluate side-chains 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 48 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.072886 restraints weight = 37004.673| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.03 r_work: 0.2978 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18497 Z= 0.133 Angle : 0.508 5.956 25090 Z= 0.272 Chirality : 0.043 0.174 2824 Planarity : 0.004 0.053 3142 Dihedral : 7.567 84.538 2833 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.98 % Allowed : 14.58 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2243 helix: 1.46 (0.18), residues: 898 sheet: -0.64 (0.28), residues: 363 loop : -1.21 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.031 0.001 TYR B 751 PHE 0.025 0.001 PHE D 235 TRP 0.014 0.001 TRP B 818 HIS 0.004 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00312 (18470) covalent geometry : angle 0.50333 (25027) SS BOND : bond 0.00216 ( 18) SS BOND : angle 1.00076 ( 36) hydrogen bonds : bond 0.05132 ( 731) hydrogen bonds : angle 4.01901 ( 2097) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 1.33530 ( 9) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.01250 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: B 117 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 336 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8373 (mptt) REVERT: B 558 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7632 (mp0) REVERT: B 609 THR cc_start: 0.8916 (m) cc_final: 0.8442 (p) REVERT: B 697 VAL cc_start: 0.7627 (t) cc_final: 0.7285 (t) REVERT: B 876 THR cc_start: 0.5219 (OUTLIER) cc_final: 0.4870 (m) REVERT: D 17 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7384 (tt0) REVERT: D 229 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8205 (mt) REVERT: D 235 PHE cc_start: 0.8076 (t80) cc_final: 0.7616 (t80) outliers start: 37 outliers final: 31 residues processed: 212 average time/residue: 0.1530 time to fit residues: 48.1388 Evaluate side-chains 221 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 198 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.089097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073570 restraints weight = 37029.145| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.03 r_work: 0.2994 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18497 Z= 0.115 Angle : 0.485 6.789 25090 Z= 0.261 Chirality : 0.042 0.167 2824 Planarity : 0.004 0.052 3142 Dihedral : 7.390 82.689 2833 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.82 % Allowed : 14.74 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.18), residues: 2243 helix: 1.54 (0.18), residues: 897 sheet: -0.59 (0.27), residues: 367 loop : -1.19 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 54 TYR 0.029 0.001 TYR B 751 PHE 0.023 0.001 PHE D 235 TRP 0.013 0.001 TRP B 818 HIS 0.003 0.001 HIS B 766 Details of bonding type rmsd covalent geometry : bond 0.00264 (18470) covalent geometry : angle 0.48124 (25027) SS BOND : bond 0.00218 ( 18) SS BOND : angle 0.99535 ( 36) hydrogen bonds : bond 0.04668 ( 731) hydrogen bonds : angle 3.93603 ( 2097) link_BETA1-4 : bond 0.00292 ( 3) link_BETA1-4 : angle 1.27804 ( 9) link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.88960 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4610.78 seconds wall clock time: 79 minutes 27.82 seconds (4767.82 seconds total)