Starting phenix.real_space_refine on Sun Aug 24 17:28:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thf_41260/08_2025/8thf_41260.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thf_41260/08_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_41260/08_2025/8thf_41260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thf_41260/08_2025/8thf_41260.map" model { file = "/net/cci-nas-00/data/ceres_data/8thf_41260/08_2025/8thf_41260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thf_41260/08_2025/8thf_41260.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.57, per 1000 atoms: 0.40 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: 1.59 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.90 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: 4.59 Time building geometry restraints manager: 2.20 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 1303)) selection = (chain 'B' and (resid 14 through 625 or resid 627 through 631 or resid 652 throu \ gh 821 or resid 823 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 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: 3.570 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 24.290 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.048 0.002 ARG B 76 TYR 0.057 0.004 TYR A 559 PHE 0.126 0.006 PHE B 131 TRP 0.065 0.006 TRP A 255 HIS 0.032 0.003 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.01139 (22001) covalent geometry : angle 1.41821 (29946) SS BOND : bond 0.00955 ( 30) SS BOND : angle 4.07963 ( 60) hydrogen bonds : bond 0.13760 ( 833) hydrogen bonds : angle 7.18935 ( 2304) link_BETA1-4 : bond 0.00583 ( 12) link_BETA1-4 : angle 2.45350 ( 36) link_NAG-ASN : bond 0.01497 ( 27) link_NAG-ASN : angle 7.58820 ( 81) *********************** 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 : 0.740 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: 0.5835 time to fit residues: 82.5173 Evaluate side-chains 69 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 704 GLN C 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067040 restraints weight = 93050.193| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.70 r_work: 0.2919 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22070 Z= 0.143 Angle : 0.795 16.542 30123 Z= 0.391 Chirality : 0.049 0.358 3543 Planarity : 0.006 0.080 3818 Dihedral : 10.921 95.576 3684 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 0.68 % Allowed : 4.61 % Favored : 94.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.15), residues: 2660 helix: 0.73 (0.21), residues: 597 sheet: 0.15 (0.21), residues: 572 loop : -2.46 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 786 TYR 0.025 0.001 TYR C 165 PHE 0.022 0.002 PHE B 362 TRP 0.027 0.002 TRP C 102 HIS 0.003 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00319 (22001) covalent geometry : angle 0.74477 (29946) SS BOND : bond 0.00358 ( 30) SS BOND : angle 1.65866 ( 60) hydrogen bonds : bond 0.04681 ( 833) hydrogen bonds : angle 5.65451 ( 2304) link_BETA1-4 : bond 0.00593 ( 12) link_BETA1-4 : angle 1.95635 ( 36) link_NAG-ASN : bond 0.00536 ( 27) link_NAG-ASN : angle 5.13136 ( 81) *********************** 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 108 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 559 TYR cc_start: 0.8363 (m-80) cc_final: 0.8009 (m-80) REVERT: A 941 TYR cc_start: 0.8260 (t80) cc_final: 0.7777 (t80) REVERT: B 172 MET cc_start: 0.2156 (mmm) cc_final: 0.1632 (mpm) REVERT: B 941 TYR cc_start: 0.8222 (t80) cc_final: 0.7877 (t80) REVERT: C 367 GLN cc_start: 0.6700 (pt0) cc_final: 0.6326 (pt0) REVERT: C 941 TYR cc_start: 0.8133 (t80) cc_final: 0.7781 (t80) outliers start: 16 outliers final: 4 residues processed: 98 average time/residue: 0.4867 time to fit residues: 56.4753 Evaluate side-chains 75 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 797 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 175 optimal weight: 2.9990 chunk 79 optimal weight: 0.0010 chunk 113 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 105 optimal weight: 0.0030 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 17 ASN B 339 ASN B 461 ASN C 113 GLN C 345 ASN C 704 GLN C 805 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.067083 restraints weight = 92660.989| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.66 r_work: 0.2941 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22070 Z= 0.138 Angle : 0.708 14.036 30123 Z= 0.348 Chirality : 0.048 0.513 3543 Planarity : 0.005 0.069 3818 Dihedral : 8.522 86.583 3684 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 0.80 % Allowed : 6.26 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 2660 helix: 1.75 (0.21), residues: 601 sheet: 0.30 (0.22), residues: 556 loop : -2.29 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 786 TYR 0.018 0.001 TYR C 870 PHE 0.019 0.001 PHE A 138 TRP 0.024 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00315 (22001) covalent geometry : angle 0.67099 (29946) SS BOND : bond 0.00283 ( 30) SS BOND : angle 1.51348 ( 60) hydrogen bonds : bond 0.04339 ( 833) hydrogen bonds : angle 5.16246 ( 2304) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 1.52826 ( 36) link_NAG-ASN : bond 0.00677 ( 27) link_NAG-ASN : angle 4.17352 ( 81) *********************** 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 113 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8265 (t80) cc_final: 0.7842 (t80) REVERT: A 947 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8523 (mp0) REVERT: B 172 MET cc_start: 0.2212 (mmm) cc_final: 0.1720 (mpm) REVERT: B 805 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (mp10) REVERT: B 941 TYR cc_start: 0.8232 (t80) cc_final: 0.7951 (t80) REVERT: C 148 MET cc_start: 0.8843 (mmm) cc_final: 0.8543 (mmm) REVERT: C 367 GLN cc_start: 0.6619 (pt0) cc_final: 0.6041 (pm20) REVERT: C 805 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: C 895 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (pm20) REVERT: C 941 TYR cc_start: 0.8238 (t80) cc_final: 0.7874 (t80) outliers start: 19 outliers final: 4 residues processed: 103 average time/residue: 0.4625 time to fit residues: 56.5086 Evaluate side-chains 86 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain C residue 255 TRP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 79 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 197 optimal weight: 0.0870 chunk 131 optimal weight: 9.9990 chunk 125 optimal weight: 0.0070 chunk 104 optimal weight: 30.0000 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.112837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066940 restraints weight = 98903.464| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.77 r_work: 0.2913 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 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 = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22070 Z= 0.133 Angle : 0.691 13.253 30123 Z= 0.337 Chirality : 0.047 0.448 3543 Planarity : 0.005 0.062 3818 Dihedral : 7.794 78.290 3684 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 0.76 % Allowed : 7.36 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.16), residues: 2660 helix: 2.19 (0.21), residues: 594 sheet: 0.29 (0.22), residues: 561 loop : -2.17 (0.14), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 786 TYR 0.018 0.001 TYR B 870 PHE 0.023 0.001 PHE A 395 TRP 0.025 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00306 (22001) covalent geometry : angle 0.65499 (29946) SS BOND : bond 0.00258 ( 30) SS BOND : angle 1.32443 ( 60) hydrogen bonds : bond 0.04087 ( 833) hydrogen bonds : angle 5.04187 ( 2304) link_BETA1-4 : bond 0.00477 ( 12) link_BETA1-4 : angle 1.49637 ( 36) link_NAG-ASN : bond 0.00396 ( 27) link_NAG-ASN : angle 4.06080 ( 81) *********************** 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 103 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 941 TYR cc_start: 0.8239 (t80) cc_final: 0.7875 (t80) REVERT: A 947 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8510 (mp0) REVERT: B 172 MET cc_start: 0.2159 (mmm) cc_final: 0.1741 (mpm) REVERT: B 941 TYR cc_start: 0.8225 (t80) cc_final: 0.7936 (t80) REVERT: C 941 TYR cc_start: 0.8236 (t80) cc_final: 0.7869 (t80) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.4889 time to fit residues: 55.4680 Evaluate side-chains 87 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE 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 76 optimal weight: 2.9990 chunk 209 optimal weight: 0.4980 chunk 184 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.113112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067225 restraints weight = 99002.528| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.78 r_work: 0.2947 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22070 Z= 0.122 Angle : 0.665 12.885 30123 Z= 0.324 Chirality : 0.047 0.417 3543 Planarity : 0.004 0.056 3818 Dihedral : 7.045 66.184 3684 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.50 % Favored : 94.42 % Rotamer: Outliers : 1.01 % Allowed : 7.70 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.16), residues: 2660 helix: 2.44 (0.21), residues: 594 sheet: 0.29 (0.22), residues: 561 loop : -2.05 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 786 TYR 0.027 0.001 TYR B 165 PHE 0.019 0.001 PHE A 138 TRP 0.027 0.002 TRP A 102 HIS 0.003 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00278 (22001) covalent geometry : angle 0.63279 (29946) SS BOND : bond 0.00243 ( 30) SS BOND : angle 1.21351 ( 60) hydrogen bonds : bond 0.03910 ( 833) hydrogen bonds : angle 4.89712 ( 2304) link_BETA1-4 : bond 0.00509 ( 12) link_BETA1-4 : angle 1.53335 ( 36) link_NAG-ASN : bond 0.00374 ( 27) link_NAG-ASN : angle 3.80483 ( 81) *********************** 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 113 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7294 (t70) cc_final: 0.6981 (t70) REVERT: A 737 ILE cc_start: 0.8103 (mm) cc_final: 0.7853 (mp) REVERT: A 941 TYR cc_start: 0.8240 (t80) cc_final: 0.7925 (t80) REVERT: A 947 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8530 (mp0) REVERT: B 737 ILE cc_start: 0.8251 (mm) cc_final: 0.8014 (mp) REVERT: B 805 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8496 (mp10) REVERT: C 52 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 172 MET cc_start: -0.0434 (OUTLIER) cc_final: -0.0834 (ptp) REVERT: C 368 PHE cc_start: 0.7155 (m-80) cc_final: 0.6902 (m-80) REVERT: C 543 MET cc_start: 0.9074 (mmm) cc_final: 0.7506 (tmt) REVERT: C 941 TYR cc_start: 0.8257 (t80) cc_final: 0.7880 (t80) outliers start: 24 outliers final: 10 residues processed: 103 average time/residue: 0.4694 time to fit residues: 56.6815 Evaluate side-chains 91 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 500 MET 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 62 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 565 GLN B 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.112820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066750 restraints weight = 105129.574| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.91 r_work: 0.2909 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22070 Z= 0.133 Angle : 0.670 13.372 30123 Z= 0.327 Chirality : 0.047 0.472 3543 Planarity : 0.004 0.053 3818 Dihedral : 6.685 57.546 3684 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 0.89 % Allowed : 8.12 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2660 helix: 2.52 (0.21), residues: 593 sheet: 0.32 (0.22), residues: 555 loop : -2.01 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 786 TYR 0.018 0.001 TYR B 870 PHE 0.022 0.001 PHE A 658 TRP 0.027 0.002 TRP A 102 HIS 0.003 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00311 (22001) covalent geometry : angle 0.63680 (29946) SS BOND : bond 0.00283 ( 30) SS BOND : angle 1.74635 ( 60) hydrogen bonds : bond 0.03964 ( 833) hydrogen bonds : angle 4.86401 ( 2304) link_BETA1-4 : bond 0.00478 ( 12) link_BETA1-4 : angle 1.48074 ( 36) link_NAG-ASN : bond 0.00352 ( 27) link_NAG-ASN : angle 3.69651 ( 81) *********************** 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 108 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7286 (t70) cc_final: 0.6977 (t70) REVERT: A 77 PHE cc_start: 0.7966 (m-10) cc_final: 0.7429 (m-10) REVERT: A 737 ILE cc_start: 0.8038 (mm) cc_final: 0.7812 (mp) REVERT: A 941 TYR cc_start: 0.8234 (t80) cc_final: 0.7912 (t80) REVERT: A 947 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8525 (mp0) REVERT: B 737 ILE cc_start: 0.8211 (mm) cc_final: 0.8000 (mp) REVERT: C 52 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 172 MET cc_start: -0.0324 (OUTLIER) cc_final: -0.0906 (ptp) REVERT: C 367 GLN cc_start: 0.6593 (pt0) cc_final: 0.6382 (pt0) REVERT: C 543 MET cc_start: 0.9084 (mmm) cc_final: 0.7522 (tmt) REVERT: C 941 TYR cc_start: 0.8275 (t80) cc_final: 0.7886 (t80) outliers start: 21 outliers final: 12 residues processed: 100 average time/residue: 0.4828 time to fit residues: 56.8510 Evaluate side-chains 92 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASN 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 500 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 157 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.111807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065796 restraints weight = 95736.492| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.72 r_work: 0.2889 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22070 Z= 0.179 Angle : 0.734 24.119 30123 Z= 0.350 Chirality : 0.060 2.065 3543 Planarity : 0.004 0.051 3818 Dihedral : 6.700 57.186 3684 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 0.89 % Allowed : 8.54 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2660 helix: 2.49 (0.21), residues: 593 sheet: 0.36 (0.22), residues: 558 loop : -2.05 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 568 TYR 0.020 0.001 TYR B 870 PHE 0.027 0.002 PHE A 395 TRP 0.031 0.002 TRP A 255 HIS 0.005 0.001 HIS C 904 Details of bonding type rmsd covalent geometry : bond 0.00425 (22001) covalent geometry : angle 0.68168 (29946) SS BOND : bond 0.00276 ( 30) SS BOND : angle 1.72831 ( 60) hydrogen bonds : bond 0.04333 ( 833) hydrogen bonds : angle 4.90510 ( 2304) link_BETA1-4 : bond 0.00510 ( 12) link_BETA1-4 : angle 1.67429 ( 36) link_NAG-ASN : bond 0.00396 ( 27) link_NAG-ASN : angle 4.99249 ( 81) *********************** 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 105 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7344 (t70) cc_final: 0.7062 (t70) REVERT: A 77 PHE cc_start: 0.8142 (m-10) cc_final: 0.7851 (m-10) REVERT: A 737 ILE cc_start: 0.8165 (mm) cc_final: 0.7928 (mp) REVERT: A 941 TYR cc_start: 0.8246 (t80) cc_final: 0.7929 (t80) REVERT: A 947 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8542 (mp0) REVERT: B 737 ILE cc_start: 0.8276 (mm) cc_final: 0.8058 (mp) REVERT: B 941 TYR cc_start: 0.8251 (t80) cc_final: 0.7927 (t80) REVERT: C 52 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7794 (tm-30) REVERT: C 543 MET cc_start: 0.9095 (mmm) cc_final: 0.7550 (tmt) REVERT: C 941 TYR cc_start: 0.8267 (t80) cc_final: 0.7873 (t80) outliers start: 21 outliers final: 11 residues processed: 99 average time/residue: 0.5121 time to fit residues: 59.8795 Evaluate side-chains 88 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 776 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 42 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 250 optimal weight: 0.8980 chunk 130 optimal weight: 0.0970 chunk 162 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN A 760 GLN B 143 ASN C 113 GLN C 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.111853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066984 restraints weight = 96804.727| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.58 r_work: 0.2904 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2335 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= 0.155 Angle : 0.712 24.538 30123 Z= 0.343 Chirality : 0.052 1.293 3543 Planarity : 0.004 0.050 3818 Dihedral : 6.538 57.299 3684 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 0.93 % Allowed : 8.92 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2660 helix: 2.52 (0.21), residues: 594 sheet: 0.32 (0.22), residues: 556 loop : -2.04 (0.14), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 568 TYR 0.021 0.001 TYR C 195 PHE 0.025 0.002 PHE A 395 TRP 0.028 0.002 TRP A 102 HIS 0.004 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00364 (22001) covalent geometry : angle 0.66141 (29946) SS BOND : bond 0.00326 ( 30) SS BOND : angle 1.62635 ( 60) hydrogen bonds : bond 0.04197 ( 833) hydrogen bonds : angle 4.87834 ( 2304) link_BETA1-4 : bond 0.00495 ( 12) link_BETA1-4 : angle 1.60437 ( 36) link_NAG-ASN : bond 0.00517 ( 27) link_NAG-ASN : angle 4.88409 ( 81) *********************** 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 101 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7378 (t70) cc_final: 0.7127 (t70) REVERT: A 737 ILE cc_start: 0.8125 (mm) cc_final: 0.7911 (mp) REVERT: A 941 TYR cc_start: 0.8220 (t80) cc_final: 0.7900 (t80) REVERT: A 947 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8547 (mp0) REVERT: B 737 ILE cc_start: 0.8247 (mm) cc_final: 0.8035 (mp) REVERT: B 947 GLU cc_start: 0.9053 (tp30) cc_final: 0.8698 (mp0) REVERT: C 52 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7800 (tm-30) REVERT: C 172 MET cc_start: -0.0269 (OUTLIER) cc_final: -0.0854 (ptp) REVERT: C 543 MET cc_start: 0.9060 (mmm) cc_final: 0.7513 (tmt) REVERT: C 941 TYR cc_start: 0.8240 (t80) cc_final: 0.7839 (t80) outliers start: 22 outliers final: 12 residues processed: 95 average time/residue: 0.4445 time to fit residues: 50.4488 Evaluate side-chains 88 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 44 optimal weight: 0.0670 chunk 247 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 243 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.113237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067305 restraints weight = 102860.807| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.85 r_work: 0.2928 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2496 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= 0.113 Angle : 0.680 22.623 30123 Z= 0.326 Chirality : 0.049 0.973 3543 Planarity : 0.004 0.049 3818 Dihedral : 6.328 57.561 3684 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 0.72 % Allowed : 9.05 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.16), residues: 2660 helix: 2.63 (0.21), residues: 594 sheet: 0.32 (0.22), residues: 556 loop : -1.94 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.017 0.001 TYR C 165 PHE 0.022 0.001 PHE A 395 TRP 0.036 0.002 TRP C 102 HIS 0.003 0.000 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00253 (22001) covalent geometry : angle 0.63107 (29946) SS BOND : bond 0.00227 ( 30) SS BOND : angle 1.55582 ( 60) hydrogen bonds : bond 0.03717 ( 833) hydrogen bonds : angle 4.76225 ( 2304) link_BETA1-4 : bond 0.00460 ( 12) link_BETA1-4 : angle 1.66631 ( 36) link_NAG-ASN : bond 0.00508 ( 27) link_NAG-ASN : angle 4.63511 ( 81) *********************** 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 97 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7312 (t70) cc_final: 0.7011 (t0) REVERT: A 941 TYR cc_start: 0.8238 (t80) cc_final: 0.7921 (t80) REVERT: A 947 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8542 (mp0) REVERT: B 947 GLU cc_start: 0.9024 (tp30) cc_final: 0.8668 (mp0) REVERT: C 172 MET cc_start: -0.0322 (OUTLIER) cc_final: -0.0822 (ptp) REVERT: C 543 MET cc_start: 0.9064 (mmm) cc_final: 0.7583 (tmt) REVERT: C 737 ILE cc_start: 0.8208 (mm) cc_final: 0.7940 (mp) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.4943 time to fit residues: 54.3273 Evaluate side-chains 88 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASN 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 363 LEU Chi-restraints excluded: chain B residue 658 PHE Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 776 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 262 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066597 restraints weight = 110547.119| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.98 r_work: 0.2909 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22070 Z= 0.137 Angle : 0.692 22.169 30123 Z= 0.335 Chirality : 0.050 0.884 3543 Planarity : 0.004 0.049 3818 Dihedral : 6.277 57.203 3684 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 0.72 % Allowed : 9.13 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.16), residues: 2660 helix: 2.63 (0.21), residues: 589 sheet: 0.32 (0.22), residues: 555 loop : -1.96 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.017 0.001 TYR B 870 PHE 0.045 0.002 PHE B 131 TRP 0.042 0.002 TRP C 102 HIS 0.004 0.001 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00321 (22001) covalent geometry : angle 0.64494 (29946) SS BOND : bond 0.00234 ( 30) SS BOND : angle 1.59682 ( 60) hydrogen bonds : bond 0.03874 ( 833) hydrogen bonds : angle 4.79659 ( 2304) link_BETA1-4 : bond 0.00456 ( 12) link_BETA1-4 : angle 1.61297 ( 36) link_NAG-ASN : bond 0.00502 ( 27) link_NAG-ASN : angle 4.59946 ( 81) ********************** 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: 17 poor density : 73 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7315 (t70) cc_final: 0.7005 (t0) REVERT: A 941 TYR cc_start: 0.8245 (t80) cc_final: 0.7919 (t80) REVERT: A 947 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8553 (mp0) REVERT: B 947 GLU cc_start: 0.9028 (tp30) cc_final: 0.8665 (mp0) REVERT: C 172 MET cc_start: -0.0350 (OUTLIER) cc_final: -0.0881 (ptp) REVERT: C 543 MET cc_start: 0.9069 (mmm) cc_final: 0.7591 (tmt) REVERT: C 737 ILE cc_start: 0.8239 (mm) cc_final: 0.7970 (mp) REVERT: C 895 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8818 (pm20) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.5685 time to fit residues: 56.4751 Evaluate side-chains 87 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 895 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 92 optimal weight: 0.9990 chunk 251 optimal weight: 0.0170 chunk 197 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 185 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 259 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN B 132 GLN B 345 ASN B 805 GLN B 813 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.116106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070892 restraints weight = 127931.338| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.19 r_work: 0.3008 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22070 Z= 0.106 Angle : 0.662 20.805 30123 Z= 0.320 Chirality : 0.048 0.739 3543 Planarity : 0.004 0.049 3818 Dihedral : 6.176 57.608 3684 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 0.85 % Allowed : 9.18 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2660 helix: 2.78 (0.21), residues: 592 sheet: 0.25 (0.22), residues: 558 loop : -1.87 (0.15), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.017 0.001 TYR C 195 PHE 0.024 0.001 PHE B 131 TRP 0.046 0.002 TRP C 102 HIS 0.002 0.000 HIS C 757 Details of bonding type rmsd covalent geometry : bond 0.00228 (22001) covalent geometry : angle 0.61864 (29946) SS BOND : bond 0.00197 ( 30) SS BOND : angle 1.32808 ( 60) hydrogen bonds : bond 0.03333 ( 833) hydrogen bonds : angle 4.67442 ( 2304) link_BETA1-4 : bond 0.00474 ( 12) link_BETA1-4 : angle 1.69470 ( 36) link_NAG-ASN : bond 0.00538 ( 27) link_NAG-ASN : angle 4.32887 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8499.45 seconds wall clock time: 145 minutes 11.09 seconds (8711.09 seconds total)