Starting phenix.real_space_refine on Wed Jun 18 20:25:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thf_41260/06_2025/8thf_41260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thf_41260/06_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_41260/06_2025/8thf_41260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thf_41260/06_2025/8thf_41260.map" model { file = "/net/cci-nas-00/data/ceres_data/8thf_41260/06_2025/8thf_41260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thf_41260/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 22.45, per 1000 atoms: 1.04 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: 5.22 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: 2.88 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: 8.80 Time building geometry restraints manager: 6.23 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: 23.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 63.420 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.190 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.780 ------------------------------------------------------------------------------- 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 : 2.384 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: 1.2365 time to fit residues: 175.6057 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 : 2.344 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066596 restraints weight = 116133.212| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.13 r_work: 0.2925 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 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 = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 2.500 Fit side-chains revert: symmetry clash REVERT: A 559 TYR cc_start: 0.8362 (m-80) cc_final: 0.8027 (m-80) REVERT: A 941 TYR cc_start: 0.8275 (t80) cc_final: 0.7784 (t80) REVERT: B 172 MET cc_start: 0.2195 (mmm) cc_final: 0.1509 (mpm) REVERT: B 941 TYR cc_start: 0.8241 (t80) cc_final: 0.7891 (t80) REVERT: C 367 GLN cc_start: 0.6827 (pt0) cc_final: 0.6432 (pt0) REVERT: C 941 TYR cc_start: 0.8149 (t80) cc_final: 0.7779 (t80) outliers start: 18 outliers final: 5 residues processed: 102 average time/residue: 1.1027 time to fit residues: 134.3967 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 : 2.644 ------------------------------------------------------------------------------- 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: 4.9990 chunk 3 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.110323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063693 restraints weight = 94420.753| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.70 r_work: 0.2873 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22070 Z= 0.246 Angle : 0.792 15.564 30123 Z= 0.392 Chirality : 0.051 0.457 3543 Planarity : 0.005 0.071 3818 Dihedral : 9.264 94.587 3684 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 0.72 % Allowed : 6.30 % Favored : 92.98 % 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: -1.21 (0.16), residues: 2660 helix: 1.63 (0.21), residues: 595 sheet: 0.23 (0.21), residues: 555 loop : -2.39 (0.14), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 689 HIS 0.006 0.001 HIS C 757 PHE 0.035 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 0.00500 ( 27) link_NAG-ASN : angle 4.60290 ( 81) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.53030 ( 36) hydrogen bonds : bond 0.05429 ( 833) hydrogen bonds : angle 5.42177 ( 2304) SS BOND : bond 0.00362 ( 30) SS BOND : angle 1.90783 ( 60) covalent geometry : bond 0.00588 (22001) covalent geometry : angle 0.75061 (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 101 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8267 (t80) cc_final: 0.7857 (t80) REVERT: A 947 GLU cc_start: 0.8454 (mp0) cc_final: 0.8203 (OUTLIER) REVERT: B 172 MET cc_start: 0.2134 (mmm) cc_final: 0.1605 (mpm) REVERT: B 941 TYR cc_start: 0.8264 (t80) cc_final: 0.7954 (t80) REVERT: C 77 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: C 367 GLN cc_start: 0.6837 (pt0) cc_final: 0.6563 (pt0) REVERT: C 895 GLU cc_start: 0.8971 (pt0) cc_final: 0.8680 (pm20) REVERT: C 941 TYR cc_start: 0.8259 (t80) cc_final: 0.7871 (t80) outliers start: 17 outliers final: 8 residues processed: 93 average time/residue: 1.4420 time to fit residues: 160.7038 Evaluate side-chains 82 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 763 ASN 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 77 PHE 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: 2.9990 chunk 156 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN B 339 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.112438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066839 restraints weight = 83359.360| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.45 r_work: 0.2942 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22070 Z= 0.129 Angle : 0.690 13.646 30123 Z= 0.339 Chirality : 0.047 0.415 3543 Planarity : 0.005 0.063 3818 Dihedral : 8.061 84.366 3684 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.72 % Allowed : 7.27 % Favored : 92.01 % 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: -0.91 (0.16), residues: 2660 helix: 2.12 (0.21), residues: 593 sheet: 0.21 (0.22), residues: 550 loop : -2.20 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 PHE 0.021 0.001 PHE A 138 TYR 0.020 0.001 TYR C 165 ARG 0.005 0.000 ARG B 894 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 27) link_NAG-ASN : angle 4.14208 ( 81) link_BETA1-4 : bond 0.00510 ( 12) link_BETA1-4 : angle 1.50527 ( 36) hydrogen bonds : bond 0.04120 ( 833) hydrogen bonds : angle 5.09522 ( 2304) SS BOND : bond 0.00286 ( 30) SS BOND : angle 1.40184 ( 60) covalent geometry : bond 0.00291 (22001) covalent geometry : angle 0.65261 (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 107 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8226 (t80) cc_final: 0.7871 (t80) REVERT: A 947 GLU cc_start: 0.8471 (mp0) cc_final: 0.8171 (mp0) REVERT: B 172 MET cc_start: 0.2393 (mmm) cc_final: 0.1981 (mpm) REVERT: B 941 TYR cc_start: 0.8236 (t80) cc_final: 0.7965 (t80) REVERT: C 368 PHE cc_start: 0.6676 (m-10) cc_final: 0.6474 (m-80) REVERT: C 941 TYR cc_start: 0.8238 (t80) cc_final: 0.7877 (t80) outliers start: 17 outliers final: 11 residues processed: 101 average time/residue: 1.0866 time to fit residues: 131.6760 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 : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 763 ASN 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: 4.9990 chunk 224 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 179 optimal weight: 40.0000 chunk 169 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.111578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.065113 restraints weight = 98908.238| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.78 r_work: 0.2906 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22070 Z= 0.158 Angle : 0.698 13.138 30123 Z= 0.341 Chirality : 0.048 0.421 3543 Planarity : 0.005 0.059 3818 Dihedral : 7.526 77.196 3684 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 1.14 % Allowed : 7.44 % Favored : 91.42 % 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: -0.76 (0.16), residues: 2660 helix: 2.31 (0.21), residues: 592 sheet: 0.28 (0.22), residues: 560 loop : -2.14 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 PHE 0.024 0.002 PHE A 395 TYR 0.024 0.001 TYR B 165 ARG 0.003 0.000 ARG B 568 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 27) link_NAG-ASN : angle 3.97037 ( 81) link_BETA1-4 : bond 0.00425 ( 12) link_BETA1-4 : angle 1.49651 ( 36) hydrogen bonds : bond 0.04400 ( 833) hydrogen bonds : angle 5.04588 ( 2304) SS BOND : bond 0.00276 ( 30) SS BOND : angle 1.41572 ( 60) covalent geometry : bond 0.00373 (22001) covalent geometry : angle 0.66437 (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 109 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7372 (t70) cc_final: 0.7053 (t70) REVERT: A 941 TYR cc_start: 0.8274 (t80) cc_final: 0.7919 (t80) REVERT: A 947 GLU cc_start: 0.8526 (mp0) cc_final: 0.8186 (mp0) REVERT: B 172 MET cc_start: 0.2200 (mmm) cc_final: 0.1947 (mpm) REVERT: B 805 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: C 77 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7662 (m-10) REVERT: C 172 MET cc_start: -0.0220 (OUTLIER) cc_final: -0.0684 (ptp) REVERT: C 368 PHE cc_start: 0.6840 (m-10) cc_final: 0.6634 (m-80) REVERT: C 941 TYR cc_start: 0.8276 (t80) cc_final: 0.7902 (t80) outliers start: 27 outliers final: 11 residues processed: 101 average time/residue: 1.1163 time to fit residues: 134.0019 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 : 2.477 ------------------------------------------------------------------------------- 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 776 ILE Chi-restraints excluded: chain A residue 901 ASN 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 Chi-restraints excluded: chain C residue 737 ILE 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: 0.9980 chunk 202 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.111306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066692 restraints weight = 80790.597| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 4.29 r_work: 0.2925 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 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 = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22070 Z= 0.163 Angle : 0.699 12.939 30123 Z= 0.342 Chirality : 0.048 0.416 3543 Planarity : 0.004 0.055 3818 Dihedral : 7.192 71.263 3684 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % 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: -0.72 (0.16), residues: 2660 helix: 2.40 (0.21), residues: 593 sheet: 0.27 (0.22), residues: 559 loop : -2.12 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 PHE 0.025 0.001 PHE A 395 TYR 0.018 0.001 TYR B 870 ARG 0.003 0.000 ARG B 786 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 27) link_NAG-ASN : angle 3.89649 ( 81) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 1.49429 ( 36) hydrogen bonds : bond 0.04405 ( 833) hydrogen bonds : angle 5.02563 ( 2304) SS BOND : bond 0.00272 ( 30) SS BOND : angle 1.85009 ( 60) covalent geometry : bond 0.00388 (22001) covalent geometry : angle 0.66415 (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 109 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7976 (m-10) cc_final: 0.7430 (m-10) REVERT: A 941 TYR cc_start: 0.8239 (t80) cc_final: 0.7917 (t80) REVERT: A 947 GLU cc_start: 0.8558 (mp0) cc_final: 0.8194 (mp0) REVERT: B 737 ILE cc_start: 0.8361 (mm) cc_final: 0.8081 (mp) REVERT: C 77 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7685 (m-10) REVERT: C 163 PHE cc_start: 0.6515 (t80) cc_final: 0.5996 (t80) REVERT: C 543 MET cc_start: 0.9112 (mmm) cc_final: 0.7560 (tmt) REVERT: C 604 ASN cc_start: 0.9343 (OUTLIER) cc_final: 0.9119 (p0) REVERT: C 941 TYR cc_start: 0.8279 (t80) cc_final: 0.7890 (t80) outliers start: 25 outliers final: 10 residues processed: 101 average time/residue: 1.0569 time to fit residues: 127.5961 Evaluate side-chains 88 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 205 ILE Chi-restraints excluded: chain B residue 542 THR 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 604 ASN Chi-restraints excluded: chain C residue 737 ILE 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: 1.9990 chunk 208 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN B 805 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.111020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065040 restraints weight = 94985.794| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.65 r_work: 0.2916 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22070 Z= 0.219 Angle : 0.765 25.077 30123 Z= 0.366 Chirality : 0.060 1.963 3543 Planarity : 0.005 0.058 3818 Dihedral : 7.261 67.369 3684 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 1.01 % Allowed : 8.33 % Favored : 90.66 % 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: -0.77 (0.16), residues: 2660 helix: 2.37 (0.21), residues: 593 sheet: 0.21 (0.22), residues: 559 loop : -2.14 (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 0.028 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 0.00445 ( 27) link_NAG-ASN : angle 5.26852 ( 81) link_BETA1-4 : bond 0.00404 ( 12) link_BETA1-4 : angle 1.60406 ( 36) hydrogen bonds : bond 0.04817 ( 833) hydrogen bonds : angle 5.07891 ( 2304) SS BOND : bond 0.00316 ( 30) SS BOND : angle 1.89468 ( 60) covalent geometry : bond 0.00523 (22001) covalent geometry : angle 0.70935 (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 102 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8222 (m-10) cc_final: 0.7965 (m-10) REVERT: A 941 TYR cc_start: 0.8247 (t80) cc_final: 0.7932 (t80) REVERT: A 947 GLU cc_start: 0.8553 (mp0) cc_final: 0.8161 (mp0) REVERT: B 737 ILE cc_start: 0.8437 (mm) cc_final: 0.8152 (mp) REVERT: B 947 GLU cc_start: 0.9025 (tp30) cc_final: 0.8678 (mp0) REVERT: C 53 ASP cc_start: 0.7153 (t0) cc_final: 0.6943 (t0) REVERT: C 77 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: C 148 MET cc_start: 0.9001 (mmp) cc_final: 0.8610 (pp-130) REVERT: C 163 PHE cc_start: 0.6617 (t80) cc_final: 0.6058 (t80) REVERT: C 543 MET cc_start: 0.9120 (mmm) cc_final: 0.7557 (tmt) REVERT: C 941 TYR cc_start: 0.8262 (t80) cc_final: 0.7867 (t80) outliers start: 23 outliers final: 11 residues processed: 94 average time/residue: 1.0162 time to fit residues: 115.2628 Evaluate side-chains 86 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 542 THR 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 737 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** C 704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.111515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065608 restraints weight = 98497.277| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.72 r_work: 0.2926 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22070 Z= 0.167 Angle : 0.731 24.816 30123 Z= 0.350 Chirality : 0.053 1.256 3543 Planarity : 0.004 0.053 3818 Dihedral : 7.016 60.326 3684 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 0.89 % Allowed : 8.50 % Favored : 90.61 % 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: -0.72 (0.16), residues: 2660 helix: 2.44 (0.21), residues: 593 sheet: 0.24 (0.22), residues: 559 loop : -2.12 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 102 HIS 0.004 0.001 HIS C 757 PHE 0.026 0.002 PHE A 395 TYR 0.018 0.001 TYR B 870 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 27) link_NAG-ASN : angle 5.21913 ( 81) link_BETA1-4 : bond 0.00512 ( 12) link_BETA1-4 : angle 1.55552 ( 36) hydrogen bonds : bond 0.04449 ( 833) hydrogen bonds : angle 4.99912 ( 2304) SS BOND : bond 0.00277 ( 30) SS BOND : angle 1.65974 ( 60) covalent geometry : bond 0.00395 (22001) covalent geometry : angle 0.67448 (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 98 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8209 (t80) cc_final: 0.7888 (t80) REVERT: A 947 GLU cc_start: 0.8543 (mp0) cc_final: 0.8118 (mp0) REVERT: B 737 ILE cc_start: 0.8367 (mm) cc_final: 0.8103 (mp) REVERT: B 947 GLU cc_start: 0.9020 (tp30) cc_final: 0.8676 (mp0) REVERT: C 77 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: C 148 MET cc_start: 0.9010 (mmp) cc_final: 0.8580 (pp-130) REVERT: C 163 PHE cc_start: 0.6623 (t80) cc_final: 0.6035 (t80) REVERT: C 368 PHE cc_start: 0.7157 (m-80) cc_final: 0.6827 (m-80) REVERT: C 543 MET cc_start: 0.9095 (mmm) cc_final: 0.7521 (tmt) REVERT: C 895 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8765 (pm20) REVERT: C 941 TYR cc_start: 0.8247 (t80) cc_final: 0.7843 (t80) outliers start: 20 outliers final: 12 residues processed: 91 average time/residue: 1.0702 time to fit residues: 117.2296 Evaluate side-chains 88 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 805 GLN 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 737 ILE 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: 0.7980 chunk 102 optimal weight: 40.0000 chunk 51 optimal weight: 0.2980 chunk 262 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 91 optimal weight: 0.0020 chunk 174 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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** C 704 GLN C 805 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.111699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066365 restraints weight = 80004.513| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.26 r_work: 0.2955 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 22070 Z= 0.181 Angle : 0.855 59.188 30123 Z= 0.445 Chirality : 0.052 1.207 3543 Planarity : 0.005 0.073 3818 Dihedral : 7.017 60.672 3684 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 0.76 % Allowed : 8.58 % Favored : 90.66 % Cbeta Deviations : 0.04 % 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: -0.70 (0.16), residues: 2660 helix: 2.46 (0.21), residues: 592 sheet: 0.24 (0.22), residues: 559 loop : -2.11 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 102 HIS 0.003 0.001 HIS C 757 PHE 0.110 0.002 PHE B 131 TYR 0.102 0.002 TYR B 155 ARG 0.002 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 27) link_NAG-ASN : angle 5.17104 ( 81) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.54830 ( 36) hydrogen bonds : bond 0.04432 ( 833) hydrogen bonds : angle 5.00284 ( 2304) SS BOND : bond 0.00290 ( 30) SS BOND : angle 2.00039 ( 60) covalent geometry : bond 0.00429 (22001) covalent geometry : angle 0.80745 (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 93 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8189 (t80) cc_final: 0.7865 (t80) REVERT: A 947 GLU cc_start: 0.8551 (mp0) cc_final: 0.8123 (mp0) REVERT: B 737 ILE cc_start: 0.8365 (mm) cc_final: 0.8102 (mp) REVERT: B 805 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8330 (mm-40) REVERT: B 947 GLU cc_start: 0.9038 (tp30) cc_final: 0.8686 (mp0) REVERT: C 77 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: C 148 MET cc_start: 0.8972 (mmp) cc_final: 0.8560 (pp-130) REVERT: C 163 PHE cc_start: 0.6609 (t80) cc_final: 0.5982 (t80) REVERT: C 172 MET cc_start: -0.0066 (OUTLIER) cc_final: -0.0484 (ptp) REVERT: C 543 MET cc_start: 0.9086 (mmm) cc_final: 0.7512 (tmt) REVERT: C 895 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: C 941 TYR cc_start: 0.8231 (t80) cc_final: 0.7814 (t80) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 1.1688 time to fit residues: 120.4486 Evaluate side-chains 91 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 737 ILE Chi-restraints excluded: chain C residue 805 GLN 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: 8.9990 chunk 167 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 0.0010 chunk 205 optimal weight: 0.0370 chunk 158 optimal weight: 7.9990 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.0870 overall best weight: 0.2242 ------------------------------------------------------------------------------- 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** C 704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.111522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.066047 restraints weight = 95306.689| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.62 r_work: 0.2941 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.469 22070 Z= 0.312 Angle : 0.805 37.773 30123 Z= 0.405 Chirality : 0.052 1.207 3543 Planarity : 0.006 0.225 3818 Dihedral : 7.017 60.672 3684 Min Nonbonded Distance : 1.510 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 0.72 % Allowed : 8.63 % Favored : 90.66 % Cbeta Deviations : 0.04 % 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: -0.70 (0.16), residues: 2660 helix: 2.46 (0.21), residues: 592 sheet: 0.24 (0.22), residues: 559 loop : -2.11 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 102 HIS 0.003 0.001 HIS C 757 PHE 0.110 0.002 PHE B 131 TYR 0.102 0.002 TYR B 155 ARG 0.002 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 27) link_NAG-ASN : angle 5.17097 ( 81) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.54859 ( 36) hydrogen bonds : bond 0.04432 ( 833) hydrogen bonds : angle 5.00282 ( 2304) SS BOND : bond 0.00290 ( 30) SS BOND : angle 2.00002 ( 60) covalent geometry : bond 0.00706 (22001) covalent geometry : angle 0.75403 (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 90 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8198 (t80) cc_final: 0.7875 (t80) REVERT: A 947 GLU cc_start: 0.8544 (mp0) cc_final: 0.8117 (mp0) REVERT: B 737 ILE cc_start: 0.8370 (mm) cc_final: 0.8107 (mp) REVERT: B 947 GLU cc_start: 0.9030 (tp30) cc_final: 0.8682 (mp0) REVERT: C 77 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: C 148 MET cc_start: 0.8996 (mmp) cc_final: 0.8568 (pp-130) REVERT: C 163 PHE cc_start: 0.6615 (t80) cc_final: 0.5977 (t80) REVERT: C 172 MET cc_start: -0.0031 (OUTLIER) cc_final: -0.0455 (ptp) REVERT: C 543 MET cc_start: 0.9091 (mmm) cc_final: 0.7516 (tmt) REVERT: C 895 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8757 (pm20) REVERT: C 941 TYR cc_start: 0.8243 (t80) cc_final: 0.7827 (t80) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 1.1536 time to fit residues: 115.7392 Evaluate side-chains 89 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 737 ILE Chi-restraints excluded: chain C residue 805 GLN 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: 7.9990 chunk 105 optimal weight: 0.0270 chunk 172 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 238 optimal weight: 0.0000 chunk 79 optimal weight: 0.2980 chunk 160 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.2646 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.111555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066317 restraints weight = 96525.628| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.64 r_work: 0.2938 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 22070 Z= 0.209 Angle : 0.856 59.198 30123 Z= 0.450 Chirality : 0.053 1.163 3543 Planarity : 0.005 0.113 3818 Dihedral : 7.019 60.607 3684 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 0.76 % Allowed : 8.58 % Favored : 90.66 % Cbeta Deviations : 0.08 % 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: 2.44 (0.21), residues: 592 sheet: 0.24 (0.22), residues: 559 loop : -2.11 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 102 HIS 0.003 0.001 HIS C 757 PHE 0.086 0.002 PHE B 131 TYR 0.081 0.002 TYR B 155 ARG 0.002 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 27) link_NAG-ASN : angle 5.14663 ( 81) link_BETA1-4 : bond 0.00669 ( 12) link_BETA1-4 : angle 1.53379 ( 36) hydrogen bonds : bond 0.04467 ( 833) hydrogen bonds : angle 5.00094 ( 2304) SS BOND : bond 0.00297 ( 30) SS BOND : angle 1.92478 ( 60) covalent geometry : bond 0.00472 (22001) covalent geometry : angle 0.80923 (29946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21354.57 seconds wall clock time: 371 minutes 59.93 seconds (22319.93 seconds total)