Starting phenix.real_space_refine on Wed May 21 16:00:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.map" model { file = "/net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thf_41260/05_2025/8thf_41260.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13712 2.51 5 N 3528 2.21 5 O 4179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21515 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7041 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 900, 7025 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 50, 'TRANS': 849} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 900, 7025 Classifications: {'peptide': 900} Link IDs: {'PTRANS': 50, 'TRANS': 849} Chain breaks: 3 bond proxies already assigned to first conformer: 7168 Chain: "B" Number of atoms: 6955 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 890, 6939 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 49, 'TRANS': 840} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 890, 6939 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 49, 'TRANS': 840} Chain breaks: 4 bond proxies already assigned to first conformer: 7077 Chain: "C" Number of atoms: 6973 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 892, 6957 Classifications: {'peptide': 892} Link IDs: {'PTRANS': 49, 'TRANS': 842} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 892, 6957 Classifications: {'peptide': 892} Link IDs: {'PTRANS': 49, 'TRANS': 842} Chain breaks: 4 bond proxies already assigned to first conformer: 7096 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 21.27, per 1000 atoms: 0.99 Number of scatterers: 21515 At special positions: 0 Unit cell: (154.048, 146.08, 162.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4179 8.00 N 3528 7.00 C 13712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.04 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.02 Simple disulfide: pdb=" SG CYS A 341 " - pdb=" SG CYS A 393 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 452 " distance=2.02 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 552 " distance=2.03 Simple disulfide: pdb=" SG CYS A 835 " - pdb=" SG CYS A 846 " distance=2.03 Simple disulfide: pdb=" SG CYS A 885 " - pdb=" SG CYS A 929 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.01 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 341 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 452 " distance=2.02 Simple disulfide: pdb=" SG CYS B 465 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 563 " distance=2.02 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 552 " distance=2.04 Simple disulfide: pdb=" SG CYS B 835 " - pdb=" SG CYS B 846 " distance=2.03 Simple disulfide: pdb=" SG CYS B 885 " - pdb=" SG CYS B 929 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.07 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.02 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 452 " distance=2.03 Simple disulfide: pdb=" SG CYS C 465 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 563 " distance=2.02 Simple disulfide: pdb=" SG CYS C 546 " - pdb=" SG CYS C 552 " distance=2.04 Simple disulfide: pdb=" SG CYS C 835 " - pdb=" SG CYS C 846 " distance=2.03 Simple disulfide: pdb=" SG CYS C 885 " - pdb=" SG CYS C 929 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1300 " - " ASN A 419 " " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 460 " " NAG A1303 " - " ASN A 512 " " NAG A1304 " - " ASN A 877 " " NAG B1300 " - " ASN B 61 " " NAG B1301 " - " ASN B 419 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 460 " " NAG B1304 " - " ASN B 512 " " NAG B1305 " - " ASN B 877 " " NAG C1101 " - " ASN C 419 " " NAG C1102 " - " ASN C 279 " " NAG C1103 " - " ASN C 512 " " NAG C1104 " - " ASN C 877 " " NAG D 1 " - " ASN C 520 " " NAG E 1 " - " ASN A 520 " " NAG F 1 " - " ASN A 604 " " NAG G 1 " - " ASN A 901 " " NAG H 1 " - " ASN A 937 " " NAG I 1 " - " ASN B 520 " " NAG J 1 " - " ASN B 604 " " NAG K 1 " - " ASN B 901 " " NAG L 1 " - " ASN B 937 " " NAG M 1 " - " ASN C 604 " " NAG N 1 " - " ASN C 901 " " NAG O 1 " - " ASN C 937 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 5.1 seconds 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5046 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 42 sheets defined 24.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 433 through 440 removed outlier: 4.182A pdb=" N TRP A 436 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 438 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 439 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 549 through 558 removed outlier: 3.605A pdb=" N SER A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 586 removed outlier: 3.768A pdb=" N GLN A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 removed outlier: 3.783A pdb=" N VAL A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 658 Processing helix chain 'A' and resid 669 through 687 Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.580A pdb=" N ALA A 693 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 711 Processing helix chain 'A' and resid 716 through 721 removed outlier: 3.833A pdb=" N TYR A 720 " --> pdb=" O GLN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 743 Processing helix chain 'A' and resid 748 through 768 removed outlier: 3.793A pdb=" N VAL A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 792 through 835 removed outlier: 4.174A pdb=" N GLN A 813 " --> pdb=" O THR A 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 549 through 556 Processing helix chain 'B' and resid 557 through 561 removed outlier: 5.218A pdb=" N SER B 561 " --> pdb=" O GLN B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 586 removed outlier: 4.066A pdb=" N LEU B 566 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 628 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 669 through 687 Processing helix chain 'B' and resid 689 through 693 Processing helix chain 'B' and resid 700 through 711 Processing helix chain 'B' and resid 716 through 721 Processing helix chain 'B' and resid 722 through 743 Processing helix chain 'B' and resid 748 through 768 removed outlier: 3.784A pdb=" N VAL B 754 " --> pdb=" O LYS B 750 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 785 Processing helix chain 'B' and resid 788 through 835 removed outlier: 4.729A pdb=" N VAL B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 813 " --> pdb=" O THR B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 949 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.751A pdb=" N GLU C 422 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 423 " --> pdb=" O CYS C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 419 through 423' Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 549 through 557 removed outlier: 3.630A pdb=" N LEU C 557 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 586 removed outlier: 3.631A pdb=" N LYS C 567 " --> pdb=" O CYS C 563 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 628 Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 669 through 687 Processing helix chain 'C' and resid 689 through 693 removed outlier: 3.559A pdb=" N ALA C 693 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 711 Processing helix chain 'C' and resid 715 through 721 removed outlier: 4.155A pdb=" N LEU C 719 " --> pdb=" O THR C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 743 Processing helix chain 'C' and resid 748 through 768 removed outlier: 3.779A pdb=" N VAL C 754 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 785 removed outlier: 3.683A pdb=" N ILE C 783 " --> pdb=" O VAL C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 835 removed outlier: 4.857A pdb=" N VAL C 794 " --> pdb=" O PRO C 790 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLN C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 949 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.293A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 184 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 203 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS A 202 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ALA A 219 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.097A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 5.786A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 138 removed outlier: 8.974A pdb=" N CYS A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N SER A 157 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N ASP A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 155 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 312 removed outlier: 3.960A pdb=" N GLY A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 368 through 369 removed outlier: 6.359A pdb=" N PHE A 368 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 458 removed outlier: 5.895A pdb=" N GLU A 457 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 499 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA A 475 " --> pdb=" O PRO A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 504 through 507 removed outlier: 6.687A pdb=" N ALA A 504 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LYS B 593 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN A 506 " --> pdb=" O LYS B 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 514 through 518 removed outlier: 3.590A pdb=" N THR A 879 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 521 through 531 removed outlier: 7.005A pdb=" N GLY A 862 " --> pdb=" O SER A 858 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER A 858 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 864 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 866 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER A 854 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 868 " --> pdb=" O LEU A 852 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 536 through 539 removed outlier: 4.554A pdb=" N LYS A 536 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 590 through 593 removed outlier: 5.653A pdb=" N ILE A 591 " --> pdb=" O ASN C 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 923 through 928 removed outlier: 4.733A pdb=" N ALA A 890 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.237A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE B 93 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.038A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.628A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 138 removed outlier: 6.392A pdb=" N GLN B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL B 154 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 4.254A pdb=" N VAL B 398 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN B 314 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY B 396 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 341 through 346 removed outlier: 3.768A pdb=" N PHE B 346 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 387 through 389 removed outlier: 6.438A pdb=" N GLY B 369 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 457 through 458 removed outlier: 5.991A pdb=" N GLU B 457 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR B 499 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 475 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 504 through 505 removed outlier: 6.849A pdb=" N ALA B 504 " --> pdb=" O ILE C 591 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 514 through 518 Processing sheet with id=AC8, first strand: chain 'B' and resid 521 through 531 removed outlier: 6.044A pdb=" N TYR B 870 " --> pdb=" O HIS B 851 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS B 851 " --> pdb=" O TYR B 870 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 536 through 539 removed outlier: 4.627A pdb=" N LYS B 536 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 923 through 925 Processing sheet with id=AD2, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.957A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.433A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.120A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU C 130 " --> pdb=" O CYS C 161 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 148 through 153 removed outlier: 5.743A pdb=" N GLU C 149 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS C 142 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.552A pdb=" N ILE C 427 " --> pdb=" O ARG C 316 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE C 309 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR C 402 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN C 311 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 400 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER C 313 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 342 through 343 Processing sheet with id=AD9, first strand: chain 'C' and resid 369 through 371 removed outlier: 7.143A pdb=" N GLY C 369 " --> pdb=" O ASP C 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 457 through 458 removed outlier: 5.898A pdb=" N GLU C 457 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR C 499 " --> pdb=" O GLU C 457 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 475 " --> pdb=" O PRO C 468 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 514 through 518 Processing sheet with id=AE3, first strand: chain 'C' and resid 521 through 531 removed outlier: 6.966A pdb=" N GLY C 862 " --> pdb=" O SER C 858 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER C 858 " --> pdb=" O GLY C 862 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 864 " --> pdb=" O PRO C 856 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 866 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 854 " --> pdb=" O LEU C 866 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 868 " --> pdb=" O LEU C 852 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 536 through 537 removed outlier: 4.600A pdb=" N LYS C 536 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 923 through 925 Processing sheet with id=AE6, first strand: chain 'C' and resid 897 through 899 833 hydrogen bonds defined for protein. 2304 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: 8.38 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4791 1.33 - 1.46: 7085 1.46 - 1.60: 9997 1.60 - 1.73: 6 1.73 - 1.86: 122 Bond restraints: 22001 Sorted by residual: bond pdb=" C VAL B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.337 1.421 -0.084 1.11e-02 8.12e+03 5.77e+01 bond pdb=" CZ TYR A 559 " pdb=" OH TYR A 559 " ideal model delta sigma weight residual 1.376 1.285 0.091 2.10e-02 2.27e+03 1.89e+01 bond pdb=" C VAL C 423 " pdb=" N PRO C 424 " ideal model delta sigma weight residual 1.332 1.367 -0.035 8.20e-03 1.49e+04 1.85e+01 bond pdb=" CA ASN A 901 " pdb=" CB ASN A 901 " ideal model delta sigma weight residual 1.531 1.465 0.066 1.56e-02 4.11e+03 1.80e+01 bond pdb=" C GLN A 318 " pdb=" N PRO A 319 " ideal model delta sigma weight residual 1.333 1.381 -0.048 1.17e-02 7.31e+03 1.70e+01 ... (remaining 21996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 29332 4.14 - 8.29: 538 8.29 - 12.43: 68 12.43 - 16.57: 6 16.57 - 20.71: 2 Bond angle restraints: 29946 Sorted by residual: angle pdb=" CA PRO A 392 " pdb=" N PRO A 392 " pdb=" CD PRO A 392 " ideal model delta sigma weight residual 112.00 98.79 13.21 1.40e+00 5.10e-01 8.90e+01 angle pdb=" N ASN A 901 " pdb=" CA ASN A 901 " pdb=" C ASN A 901 " ideal model delta sigma weight residual 112.90 102.53 10.37 1.31e+00 5.83e-01 6.26e+01 angle pdb=" N ASN B 419 " pdb=" CA ASN B 419 " pdb=" C ASN B 419 " ideal model delta sigma weight residual 109.46 98.29 11.17 1.66e+00 3.63e-01 4.53e+01 angle pdb=" C LYS B 657 " pdb=" N PHE B 658 " pdb=" CA PHE B 658 " ideal model delta sigma weight residual 122.54 111.58 10.96 1.65e+00 3.67e-01 4.41e+01 angle pdb=" C SER C 900 " pdb=" N ASN C 901 " pdb=" CA ASN C 901 " ideal model delta sigma weight residual 121.54 134.01 -12.47 1.91e+00 2.74e-01 4.26e+01 ... (remaining 29941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 12876 22.94 - 45.88: 661 45.88 - 68.81: 110 68.81 - 91.75: 41 91.75 - 114.69: 25 Dihedral angle restraints: 13713 sinusoidal: 5888 harmonic: 7825 Sorted by residual: dihedral pdb=" CA LEU C 661 " pdb=" C LEU C 661 " pdb=" N THR C 662 " pdb=" CA THR C 662 " ideal model delta harmonic sigma weight residual -180.00 -124.65 -55.35 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLY A 329 " pdb=" C GLY A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta harmonic sigma weight residual 180.00 -130.75 -49.25 0 5.00e+00 4.00e-02 9.70e+01 dihedral pdb=" CA PRO B 327 " pdb=" C PRO B 327 " pdb=" N CYS B 328 " pdb=" CA CYS B 328 " ideal model delta harmonic sigma weight residual 180.00 -131.61 -48.39 0 5.00e+00 4.00e-02 9.37e+01 ... (remaining 13710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.379: 3533 0.379 - 0.758: 8 0.758 - 1.137: 0 1.137 - 1.516: 1 1.516 - 1.895: 1 Chirality restraints: 3543 Sorted by residual: chirality pdb=" CB ILE C 653 " pdb=" CA ILE C 653 " pdb=" CG1 ILE C 653 " pdb=" CG2 ILE C 653 " both_signs ideal model delta sigma weight residual False 2.64 0.75 1.90 2.00e-01 2.50e+01 8.98e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 604 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.24 -1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" C2 NAG B1304 " pdb=" C1 NAG B1304 " pdb=" C3 NAG B1304 " pdb=" N2 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.49 -1.91 -0.59 2.00e-01 2.50e+01 8.60e+00 ... (remaining 3540 not shown) Planarity restraints: 3845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 131 " 0.054 2.00e-02 2.50e+03 5.65e-02 5.59e+01 pdb=" CG PHE B 131 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 PHE B 131 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 131 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 131 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 PHE B 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 131 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 658 " 0.053 2.00e-02 2.50e+03 5.55e-02 5.39e+01 pdb=" CG PHE B 658 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 658 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 PHE B 658 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 658 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 PHE B 658 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 658 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 901 " -0.013 2.00e-02 2.50e+03 6.42e-02 5.14e+01 pdb=" CG ASN A 901 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN A 901 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN A 901 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.056 2.00e-02 2.50e+03 ... (remaining 3842 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4616 2.78 - 3.31: 17383 3.31 - 3.84: 35318 3.84 - 4.37: 38626 4.37 - 4.90: 69628 Nonbonded interactions: 165571 Sorted by model distance: nonbonded pdb=" OE1 GLN A 132 " pdb=" OG SER A 157 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP B 371 " pdb=" OG1 THR B 375 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP C 782 " pdb=" NH1 ARG C 786 " model vdw 2.332 3.120 nonbonded pdb=" O PHE C 326 " pdb=" OG SER C 333 " model vdw 2.339 3.040 nonbonded pdb=" OE1 GLN A 768 " pdb=" OG SER A 806 " model vdw 2.341 3.040 ... (remaining 165566 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 14 through 427 or resid 438 through 625 or resid 627 throu \ gh 631 or resid 652 through 821 or resid 823 through 949 or resid 1300 through 1 \ 303)) selection = (chain 'B' and (resid 14 through 625 or resid 627 through 631 or resid 652 throu \ gh 821 or resid 823 through 949 or resid 1300 through 1303)) selection = (chain 'C' and (resid 14 through 427 or resid 438 through 625 or resid 627 throu \ gh 821 or resid 823 through 949 or resid 1101 through 1104)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.00 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: 5.320 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 60.820 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.150 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.011 0.131 22070 Z= 0.499 Angle : 1.481 29.034 30123 Z= 0.794 Chirality : 0.091 1.895 3543 Planarity : 0.011 0.156 3818 Dihedral : 15.282 114.688 8577 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.13), residues: 2660 helix: -2.55 (0.14), residues: 578 sheet: -0.11 (0.21), residues: 563 loop : -2.75 (0.13), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP A 255 HIS 0.032 0.003 HIS C 757 PHE 0.126 0.006 PHE B 131 TYR 0.057 0.004 TYR A 559 ARG 0.048 0.002 ARG B 76 Details of bonding type rmsd link_NAG-ASN : bond 0.01497 ( 27) link_NAG-ASN : angle 7.58820 ( 81) link_BETA1-4 : bond 0.00583 ( 12) link_BETA1-4 : angle 2.45350 ( 36) hydrogen bonds : bond 0.13760 ( 833) hydrogen bonds : angle 7.18935 ( 2304) SS BOND : bond 0.00955 ( 30) SS BOND : angle 4.07963 ( 60) covalent geometry : bond 0.01139 (22001) covalent geometry : angle 1.41821 (29946) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.249 Fit side-chains REVERT: A 138 PHE cc_start: 0.6620 (p90) cc_final: 0.6056 (p90) REVERT: A 214 PRO cc_start: 0.8262 (Cg_endo) cc_final: 0.7958 (Cg_exo) REVERT: B 152 PHE cc_start: 0.7196 (t80) cc_final: 0.6966 (t80) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.2191 time to fit residues: 172.9548 Evaluate side-chains 70 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 704 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN C 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066597 restraints weight = 116133.212| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.13 r_work: 0.2923 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22070 Z= 0.145 Angle : 0.796 16.678 30123 Z= 0.391 Chirality : 0.049 0.353 3543 Planarity : 0.006 0.080 3818 Dihedral : 10.868 95.408 3684 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 0.76 % Allowed : 4.44 % Favored : 94.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2660 helix: 0.66 (0.20), residues: 597 sheet: 0.16 (0.21), residues: 571 loop : -2.45 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 102 HIS 0.003 0.001 HIS A 904 PHE 0.024 0.002 PHE C 395 TYR 0.025 0.001 TYR C 165 ARG 0.008 0.001 ARG B 786 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 27) link_NAG-ASN : angle 5.11531 ( 81) link_BETA1-4 : bond 0.00554 ( 12) link_BETA1-4 : angle 1.93596 ( 36) hydrogen bonds : bond 0.04674 ( 833) hydrogen bonds : angle 5.65078 ( 2304) SS BOND : bond 0.00350 ( 30) SS BOND : angle 1.65411 ( 60) covalent geometry : bond 0.00320 (22001) covalent geometry : angle 0.74562 (29946) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.485 Fit side-chains revert: symmetry clash REVERT: A 559 TYR cc_start: 0.8361 (m-80) cc_final: 0.8030 (m-80) REVERT: A 941 TYR cc_start: 0.8274 (t80) cc_final: 0.7784 (t80) REVERT: B 172 MET cc_start: 0.2198 (mmm) cc_final: 0.1512 (mpm) REVERT: B 941 TYR cc_start: 0.8240 (t80) cc_final: 0.7893 (t80) REVERT: C 367 GLN cc_start: 0.6823 (pt0) cc_final: 0.6428 (pt0) REVERT: C 941 TYR cc_start: 0.8146 (t80) cc_final: 0.7777 (t80) outliers start: 18 outliers final: 5 residues processed: 102 average time/residue: 1.1022 time to fit residues: 134.4758 Evaluate side-chains 78 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 14 optimal weight: 5.9990 chunk 236 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 141 HIS B 461 ASN B 656 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065515 restraints weight = 96057.050| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 4.56 r_work: 0.2892 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22070 Z= 0.222 Angle : 0.775 15.387 30123 Z= 0.383 Chirality : 0.050 0.527 3543 Planarity : 0.005 0.071 3818 Dihedral : 9.067 93.313 3684 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 0.72 % Allowed : 6.26 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2660 helix: 1.66 (0.21), residues: 595 sheet: 0.26 (0.22), residues: 555 loop : -2.37 (0.14), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 689 HIS 0.006 0.001 HIS C 757 PHE 0.032 0.002 PHE B 709 TYR 0.022 0.002 TYR B 870 ARG 0.006 0.001 ARG A 437 Details of bonding type rmsd link_NAG-ASN : bond 0.00674 ( 27) link_NAG-ASN : angle 4.52521 ( 81) link_BETA1-4 : bond 0.00435 ( 12) link_BETA1-4 : angle 1.53752 ( 36) hydrogen bonds : bond 0.05302 ( 833) hydrogen bonds : angle 5.36531 ( 2304) SS BOND : bond 0.00355 ( 30) SS BOND : angle 1.85642 ( 60) covalent geometry : bond 0.00530 (22001) covalent geometry : angle 0.73436 (29946) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8257 (t80) cc_final: 0.7842 (t80) REVERT: A 947 GLU cc_start: 0.8464 (mp0) cc_final: 0.8210 (OUTLIER) REVERT: B 172 MET cc_start: 0.2103 (mmm) cc_final: 0.1565 (mpm) REVERT: B 805 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: B 941 TYR cc_start: 0.8255 (t80) cc_final: 0.7947 (t80) REVERT: C 367 GLN cc_start: 0.6821 (pt0) cc_final: 0.6561 (pt0) REVERT: C 895 GLU cc_start: 0.8942 (pt0) cc_final: 0.8690 (pm20) REVERT: C 941 TYR cc_start: 0.8252 (t80) cc_final: 0.7859 (t80) outliers start: 17 outliers final: 6 residues processed: 93 average time/residue: 1.0996 time to fit residues: 121.5712 Evaluate side-chains 81 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain C residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 263 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 240 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.113113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067740 restraints weight = 83652.875| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.44 r_work: 0.2939 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22070 Z= 0.116 Angle : 0.681 13.399 30123 Z= 0.334 Chirality : 0.047 0.397 3543 Planarity : 0.005 0.062 3818 Dihedral : 7.853 80.910 3684 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 0.68 % Allowed : 7.48 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2660 helix: 2.19 (0.21), residues: 593 sheet: 0.27 (0.22), residues: 550 loop : -2.15 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 102 HIS 0.003 0.000 HIS C 757 PHE 0.020 0.001 PHE A 138 TYR 0.022 0.001 TYR C 165 ARG 0.005 0.000 ARG B 894 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 27) link_NAG-ASN : angle 4.04125 ( 81) link_BETA1-4 : bond 0.00544 ( 12) link_BETA1-4 : angle 1.57412 ( 36) hydrogen bonds : bond 0.03880 ( 833) hydrogen bonds : angle 5.03006 ( 2304) SS BOND : bond 0.00262 ( 30) SS BOND : angle 1.26300 ( 60) covalent geometry : bond 0.00257 (22001) covalent geometry : angle 0.64509 (29946) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8226 (t80) cc_final: 0.7857 (t80) REVERT: A 947 GLU cc_start: 0.8481 (mp0) cc_final: 0.8180 (mp0) REVERT: B 172 MET cc_start: 0.2315 (mmm) cc_final: 0.1877 (mpm) REVERT: B 941 TYR cc_start: 0.8210 (t80) cc_final: 0.7922 (t80) REVERT: C 77 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: C 172 MET cc_start: -0.0381 (OUTLIER) cc_final: -0.0950 (ptp) REVERT: C 368 PHE cc_start: 0.6640 (m-10) cc_final: 0.6429 (m-80) REVERT: C 941 TYR cc_start: 0.8205 (t80) cc_final: 0.7831 (t80) outliers start: 16 outliers final: 6 residues processed: 101 average time/residue: 1.1260 time to fit residues: 134.8128 Evaluate side-chains 84 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 776 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 177 optimal weight: 0.0570 chunk 224 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 179 optimal weight: 40.0000 chunk 169 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN B 143 ASN B 760 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.111617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.065235 restraints weight = 99025.623| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 4.78 r_work: 0.2885 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22070 Z= 0.166 Angle : 0.694 15.388 30123 Z= 0.340 Chirality : 0.048 0.437 3543 Planarity : 0.004 0.057 3818 Dihedral : 7.516 76.086 3684 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 1.10 % Allowed : 7.53 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2660 helix: 2.31 (0.21), residues: 594 sheet: 0.28 (0.22), residues: 557 loop : -2.13 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 PHE 0.023 0.002 PHE A 395 TYR 0.020 0.001 TYR B 165 ARG 0.004 0.000 ARG B 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 27) link_NAG-ASN : angle 4.02111 ( 81) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.47679 ( 36) hydrogen bonds : bond 0.04350 ( 833) hydrogen bonds : angle 5.02182 ( 2304) SS BOND : bond 0.00271 ( 30) SS BOND : angle 1.38890 ( 60) covalent geometry : bond 0.00394 (22001) covalent geometry : angle 0.65915 (29946) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8262 (t80) cc_final: 0.7850 (t80) REVERT: A 947 GLU cc_start: 0.8517 (mp0) cc_final: 0.8194 (mp0) REVERT: B 172 MET cc_start: 0.2153 (mmm) cc_final: 0.1893 (mpm) REVERT: B 737 ILE cc_start: 0.8351 (mm) cc_final: 0.8059 (mp) REVERT: B 941 TYR cc_start: 0.8236 (t80) cc_final: 0.7957 (t80) REVERT: C 77 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: C 172 MET cc_start: -0.0239 (OUTLIER) cc_final: -0.0770 (ptp) REVERT: C 368 PHE cc_start: 0.6790 (m-10) cc_final: 0.6589 (m-80) REVERT: C 941 TYR cc_start: 0.8273 (t80) cc_final: 0.7897 (t80) outliers start: 26 outliers final: 8 residues processed: 98 average time/residue: 1.0642 time to fit residues: 124.2079 Evaluate side-chains 85 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 224 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.110829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064656 restraints weight = 81220.715| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.41 r_work: 0.2903 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22070 Z= 0.187 Angle : 0.710 15.738 30123 Z= 0.348 Chirality : 0.048 0.415 3543 Planarity : 0.004 0.054 3818 Dihedral : 7.181 69.958 3684 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 1.06 % Allowed : 8.03 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2660 helix: 2.38 (0.21), residues: 593 sheet: 0.25 (0.22), residues: 559 loop : -2.13 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 102 HIS 0.005 0.001 HIS C 757 PHE 0.028 0.002 PHE A 395 TYR 0.020 0.002 TYR B 870 ARG 0.003 0.000 ARG B 618 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 27) link_NAG-ASN : angle 4.03950 ( 81) link_BETA1-4 : bond 0.00434 ( 12) link_BETA1-4 : angle 1.46366 ( 36) hydrogen bonds : bond 0.04678 ( 833) hydrogen bonds : angle 5.06735 ( 2304) SS BOND : bond 0.00312 ( 30) SS BOND : angle 1.74058 ( 60) covalent geometry : bond 0.00448 (22001) covalent geometry : angle 0.67428 (29946) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8002 (m-10) cc_final: 0.7396 (m-10) REVERT: A 941 TYR cc_start: 0.8233 (t80) cc_final: 0.7908 (t80) REVERT: A 947 GLU cc_start: 0.8556 (mp0) cc_final: 0.8164 (mp0) REVERT: B 737 ILE cc_start: 0.8387 (mm) cc_final: 0.8117 (mp) REVERT: B 941 TYR cc_start: 0.8223 (t80) cc_final: 0.7934 (t80) REVERT: C 77 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: C 148 MET cc_start: 0.8982 (mmp) cc_final: 0.8651 (pp-130) REVERT: C 172 MET cc_start: -0.0210 (mtt) cc_final: -0.0620 (ptp) REVERT: C 543 MET cc_start: 0.9129 (mmm) cc_final: 0.7474 (tmt) REVERT: C 604 ASN cc_start: 0.9386 (OUTLIER) cc_final: 0.9135 (p0) REVERT: C 941 TYR cc_start: 0.8252 (t80) cc_final: 0.7854 (t80) outliers start: 25 outliers final: 9 residues processed: 102 average time/residue: 0.9912 time to fit residues: 121.8061 Evaluate side-chains 85 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 177 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.111548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065663 restraints weight = 94716.286| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.64 r_work: 0.2929 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22070 Z= 0.181 Angle : 0.741 25.218 30123 Z= 0.356 Chirality : 0.060 2.075 3543 Planarity : 0.004 0.053 3818 Dihedral : 7.126 64.854 3684 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 0.93 % Allowed : 8.63 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2660 helix: 2.43 (0.21), residues: 593 sheet: 0.24 (0.22), residues: 559 loop : -2.11 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 255 HIS 0.005 0.001 HIS C 757 PHE 0.027 0.002 PHE A 395 TYR 0.018 0.002 TYR B 870 ARG 0.004 0.000 ARG A 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 27) link_NAG-ASN : angle 5.24122 ( 81) link_BETA1-4 : bond 0.00496 ( 12) link_BETA1-4 : angle 1.58657 ( 36) hydrogen bonds : bond 0.04559 ( 833) hydrogen bonds : angle 5.01873 ( 2304) SS BOND : bond 0.00310 ( 30) SS BOND : angle 1.83705 ( 60) covalent geometry : bond 0.00428 (22001) covalent geometry : angle 0.68468 (29946) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8224 (m-10) cc_final: 0.7993 (m-10) REVERT: A 941 TYR cc_start: 0.8209 (t80) cc_final: 0.7890 (t80) REVERT: A 947 GLU cc_start: 0.8548 (mp0) cc_final: 0.8155 (mp0) REVERT: B 737 ILE cc_start: 0.8353 (mm) cc_final: 0.8076 (mp) REVERT: C 52 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 77 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: C 148 MET cc_start: 0.8954 (mmp) cc_final: 0.8600 (pp-130) REVERT: C 163 PHE cc_start: 0.6512 (t80) cc_final: 0.5887 (t80) REVERT: C 543 MET cc_start: 0.9098 (mmm) cc_final: 0.7540 (tmt) REVERT: C 604 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.9180 (p0) REVERT: C 941 TYR cc_start: 0.8245 (t80) cc_final: 0.7839 (t80) outliers start: 21 outliers final: 12 residues processed: 94 average time/residue: 0.9953 time to fit residues: 112.4752 Evaluate side-chains 89 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 144 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 32 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 805 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066266 restraints weight = 98661.707| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.73 r_work: 0.2945 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22070 Z= 0.138 Angle : 0.711 24.957 30123 Z= 0.341 Chirality : 0.052 1.330 3543 Planarity : 0.004 0.052 3818 Dihedral : 6.890 58.700 3684 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 0.89 % Allowed : 8.71 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2660 helix: 2.50 (0.21), residues: 592 sheet: 0.22 (0.22), residues: 553 loop : -2.07 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 102 HIS 0.004 0.001 HIS C 757 PHE 0.047 0.001 PHE B 658 TYR 0.017 0.001 TYR B 870 ARG 0.002 0.000 ARG A 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00502 ( 27) link_NAG-ASN : angle 5.03213 ( 81) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.57643 ( 36) hydrogen bonds : bond 0.04228 ( 833) hydrogen bonds : angle 4.95082 ( 2304) SS BOND : bond 0.00268 ( 30) SS BOND : angle 1.58353 ( 60) covalent geometry : bond 0.00321 (22001) covalent geometry : angle 0.65779 (29946) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 737 ILE cc_start: 0.8204 (mm) cc_final: 0.7935 (mp) REVERT: A 941 TYR cc_start: 0.8215 (t80) cc_final: 0.7895 (t80) REVERT: A 947 GLU cc_start: 0.8543 (mp0) cc_final: 0.8139 (mp0) REVERT: B 737 ILE cc_start: 0.8304 (mm) cc_final: 0.8054 (mp) REVERT: B 947 GLU cc_start: 0.9026 (tp30) cc_final: 0.8677 (mp0) REVERT: C 52 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 77 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: C 148 MET cc_start: 0.8924 (mmp) cc_final: 0.8564 (pp-130) REVERT: C 163 PHE cc_start: 0.6634 (t80) cc_final: 0.6078 (t80) REVERT: C 172 MET cc_start: -0.0144 (OUTLIER) cc_final: -0.0577 (ptp) REVERT: C 368 PHE cc_start: 0.7204 (m-80) cc_final: 0.6974 (m-80) REVERT: C 543 MET cc_start: 0.9089 (mmm) cc_final: 0.7520 (tmt) REVERT: C 895 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8783 (pm20) REVERT: C 941 TYR cc_start: 0.8247 (t80) cc_final: 0.7845 (t80) outliers start: 20 outliers final: 10 residues processed: 87 average time/residue: 1.1085 time to fit residues: 114.2457 Evaluate side-chains 85 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 763 ASN Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 228 optimal weight: 0.9980 chunk 102 optimal weight: 40.0000 chunk 51 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 238 optimal weight: 0.0010 chunk 114 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068234 restraints weight = 84635.854| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.44 r_work: 0.2993 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22070 Z= 0.114 Angle : 0.682 22.072 30123 Z= 0.328 Chirality : 0.049 0.879 3543 Planarity : 0.004 0.051 3818 Dihedral : 6.443 57.716 3684 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 0.97 % Allowed : 8.63 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2660 helix: 2.60 (0.21), residues: 592 sheet: 0.26 (0.22), residues: 556 loop : -1.97 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 102 HIS 0.003 0.000 HIS C 757 PHE 0.021 0.001 PHE C 368 TYR 0.018 0.001 TYR C 165 ARG 0.002 0.000 ARG C 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 27) link_NAG-ASN : angle 4.66683 ( 81) link_BETA1-4 : bond 0.00512 ( 12) link_BETA1-4 : angle 1.71421 ( 36) hydrogen bonds : bond 0.03685 ( 833) hydrogen bonds : angle 4.78653 ( 2304) SS BOND : bond 0.00207 ( 30) SS BOND : angle 1.35547 ( 60) covalent geometry : bond 0.00252 (22001) covalent geometry : angle 0.63367 (29946) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 ILE cc_start: 0.7959 (mm) cc_final: 0.7750 (mp) REVERT: A 941 TYR cc_start: 0.8218 (t80) cc_final: 0.7898 (t80) REVERT: A 947 GLU cc_start: 0.8559 (mp0) cc_final: 0.8125 (mp0) REVERT: B 947 GLU cc_start: 0.9045 (tp30) cc_final: 0.8688 (mp0) REVERT: C 77 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: C 148 MET cc_start: 0.8875 (mmp) cc_final: 0.8469 (pp-130) REVERT: C 163 PHE cc_start: 0.6732 (t80) cc_final: 0.6188 (t80) REVERT: C 172 MET cc_start: -0.0216 (OUTLIER) cc_final: -0.0690 (ptp) REVERT: C 543 MET cc_start: 0.9064 (mmm) cc_final: 0.7576 (tmt) REVERT: C 737 ILE cc_start: 0.8225 (mm) cc_final: 0.7972 (mp) REVERT: C 895 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8798 (pm20) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 1.0173 time to fit residues: 121.3840 Evaluate side-chains 90 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 10 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 205 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.113191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068200 restraints weight = 97287.021| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.66 r_work: 0.2980 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22070 Z= 0.122 Angle : 0.703 21.688 30123 Z= 0.338 Chirality : 0.049 0.796 3543 Planarity : 0.004 0.051 3818 Dihedral : 6.366 57.439 3684 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 0.72 % Allowed : 9.13 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2660 helix: 2.60 (0.21), residues: 592 sheet: 0.29 (0.22), residues: 565 loop : -1.94 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 255 HIS 0.004 0.000 HIS C 757 PHE 0.052 0.001 PHE B 131 TYR 0.024 0.001 TYR B 165 ARG 0.005 0.000 ARG B 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 27) link_NAG-ASN : angle 4.92117 ( 81) link_BETA1-4 : bond 0.00502 ( 12) link_BETA1-4 : angle 1.62963 ( 36) hydrogen bonds : bond 0.03733 ( 833) hydrogen bonds : angle 4.79408 ( 2304) SS BOND : bond 0.00230 ( 30) SS BOND : angle 1.73252 ( 60) covalent geometry : bond 0.00279 (22001) covalent geometry : angle 0.65001 (29946) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5320 Ramachandran restraints generated. 2660 Oldfield, 0 Emsley, 2660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8243 (t80) cc_final: 0.7930 (t80) REVERT: A 947 GLU cc_start: 0.8563 (mp0) cc_final: 0.8113 (mp0) REVERT: B 947 GLU cc_start: 0.9034 (tp30) cc_final: 0.8662 (mp0) REVERT: C 77 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: C 148 MET cc_start: 0.8832 (mmp) cc_final: 0.8443 (pp-130) REVERT: C 163 PHE cc_start: 0.6778 (t80) cc_final: 0.6228 (t80) REVERT: C 172 MET cc_start: -0.0048 (OUTLIER) cc_final: -0.0534 (ptp) REVERT: C 543 MET cc_start: 0.9072 (mmm) cc_final: 0.7581 (tmt) REVERT: C 737 ILE cc_start: 0.8213 (mm) cc_final: 0.7970 (mp) REVERT: C 895 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8818 (pm20) outliers start: 16 outliers final: 11 residues processed: 87 average time/residue: 1.1086 time to fit residues: 115.1917 Evaluate side-chains 91 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 211 optimal weight: 0.8980 chunk 105 optimal weight: 0.0770 chunk 172 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 79 optimal weight: 0.0370 chunk 160 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN B 345 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.112883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067171 restraints weight = 99176.295| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 4.77 r_work: 0.2924 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22070 Z= 0.122 Angle : 0.693 20.789 30123 Z= 0.333 Chirality : 0.049 0.695 3543 Planarity : 0.004 0.049 3818 Dihedral : 6.275 57.291 3684 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 0.72 % Allowed : 9.26 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2660 helix: 2.64 (0.21), residues: 593 sheet: 0.31 (0.22), residues: 556 loop : -1.92 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 102 HIS 0.004 0.000 HIS C 757 PHE 0.044 0.001 PHE C 368 TYR 0.017 0.001 TYR B 870 ARG 0.004 0.000 ARG B 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 27) link_NAG-ASN : angle 4.71564 ( 81) link_BETA1-4 : bond 0.00474 ( 12) link_BETA1-4 : angle 1.64425 ( 36) hydrogen bonds : bond 0.03733 ( 833) hydrogen bonds : angle 4.77328 ( 2304) SS BOND : bond 0.00225 ( 30) SS BOND : angle 1.61953 ( 60) covalent geometry : bond 0.00279 (22001) covalent geometry : angle 0.64347 (29946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17681.65 seconds wall clock time: 305 minutes 52.65 seconds (18352.65 seconds total)