Starting phenix.real_space_refine on Thu Aug 6 16:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.map" model { file = "/net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyd_72031/08_2026/9pyd_72031.cif" } resolution = 3.3 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= 0.019 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 110 5.16 5 C 9872 2.51 5 N 2653 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15767 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4382 Classifications: {'peptide': 555} Link IDs: {'PTRANS': 23, 'TRANS': 531} Chain breaks: 6 Chain: "B" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4306 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 7 Chain: "C" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4392 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 23, 'TRANS': 532} Chain breaks: 6 Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15767 At special positions: 0 Unit cell: (114.593, 125.65, 150.78, 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 110 16.00 O 3132 8.00 N 2653 7.00 C 9872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS C 662 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.01 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 295 " " NAG A 703 " - " ASN A 301 " " NAG A 704 " - " ASN A 332 " " NAG A 705 " - " ASN A 133 " " NAG A 706 " - " ASN A 392 " " NAG A 707 " - " ASN A 448 " " NAG A 708 " - " ASN A 197 " " NAG A 709 " - " ASN A 234 " " NAG A 710 " - " ASN A 276 " " NAG A 711 " - " ASN A 363 " " NAG B 701 " - " ASN B 197 " " NAG B 702 " - " ASN B 295 " " NAG B 703 " - " ASN B 301 " " NAG B 704 " - " ASN B 332 " " NAG B 705 " - " ASN B 133 " " NAG B 706 " - " ASN B 339 " " NAG B 707 " - " ASN B 448 " " NAG B 708 " - " ASN B 234 " " NAG B 709 " - " ASN B 276 " " NAG B 710 " - " ASN B 363 " " NAG C 701 " - " ASN C 197 " " NAG C 702 " - " ASN C 295 " " NAG C 703 " - " ASN C 301 " " NAG C 704 " - " ASN C 133 " " NAG C 705 " - " ASN C 339 " " NAG C 706 " - " ASN C 392 " " NAG C 707 " - " ASN C 448 " " NAG C 708 " - " ASN C 88 " " NAG C 709 " - " ASN C 156 " " NAG C 710 " - " ASN C 234 " " NAG C 711 " - " ASN C 276 " " NAG C 712 " - " ASN C 386 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN B 160 " " NAG I 1 " - " ASN B 156 " " NAG J 1 " - " ASN B 262 " " NAG K 1 " - " ASN B 386 " " NAG M 1 " - " ASN C 160 " " NAG N 1 " - " ASN C 332 " " NAG O 1 " - " ASN C 262 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 648.1 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 28 sheets defined 22.7% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.245A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 351 removed outlier: 4.112A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.740A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 529 through 542 removed outlier: 5.839A pdb=" N THR A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.769A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.521A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 4.102A pdb=" N GLU A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.337A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.664A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.748A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.643A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.162A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 4.231A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.574A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.773A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.553A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.808A pdb=" N CYS C 74 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.514A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.512A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.896A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.764A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 481 removed outlier: 4.020A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 536 Processing helix chain 'C' and resid 536 through 543 removed outlier: 4.188A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 546 No H-bonds generated for 'chain 'C' and resid 544 through 546' Processing helix chain 'C' and resid 569 through 597 Processing helix chain 'C' and resid 618 through 626 removed outlier: 4.006A pdb=" N ILE C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.577A pdb=" N ILE C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 645 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.686A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.529A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 4.188A pdb=" N VAL A 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.328A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.880A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 4.256A pdb=" N ALA A 433 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 261 current: chain 'A' and resid 284 through 298 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 333 current: chain 'A' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 393 through 395 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.206A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.262A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.613A pdb=" N SER B 56 " --> pdb=" O VAL B 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.659A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 133 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 177 current: chain 'H' and resid 44 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100G through 103 Processing sheet with id=AB6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB7, first strand: chain 'B' and resid 200 through 203 Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 298 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 330 through 333 current: chain 'B' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 381 through 385 current: chain 'B' and resid 466 through 470 Processing sheet with id=AB9, first strand: chain 'B' and resid 302 through 312 removed outlier: 3.848A pdb=" N ASP B 322 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LYS B 305 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TYR B 318 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE B 309 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA B 316 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AC2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.619A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 133 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 173 current: chain 'C' and resid 190 through 193 Processing sheet with id=AC6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.860A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 7.102A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.372A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1194 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: 2.90 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4233 1.33 - 1.47: 4660 1.47 - 1.60: 7030 1.60 - 1.73: 1 1.73 - 1.87: 149 Bond restraints: 16073 Sorted by residual: bond pdb=" C ILE L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.412 -0.078 2.34e-02 1.83e+03 1.11e+01 bond pdb=" N ASN C 363 " pdb=" CA ASN C 363 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.79e+00 bond pdb=" N CYS C 385 " pdb=" CA CYS C 385 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.19e-02 7.06e+03 7.30e+00 bond pdb=" N ASN C 386 " pdb=" CA ASN C 386 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.30e+00 bond pdb=" N SER C 365 " pdb=" CA SER C 365 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.32e-02 5.74e+03 6.78e+00 ... (remaining 16068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 21245 3.38 - 6.76: 492 6.76 - 10.14: 60 10.14 - 13.52: 10 13.52 - 16.90: 6 Bond angle restraints: 21813 Sorted by residual: angle pdb=" CA CYS A 378 " pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " ideal model delta sigma weight residual 114.40 129.64 -15.24 2.30e+00 1.89e-01 4.39e+01 angle pdb=" CA CYS B 296 " pdb=" CB CYS B 296 " pdb=" SG CYS B 296 " ideal model delta sigma weight residual 114.40 129.60 -15.20 2.30e+00 1.89e-01 4.37e+01 angle pdb=" CG1 ILE L 94 " pdb=" CB ILE L 94 " pdb=" CG2 ILE L 94 " ideal model delta sigma weight residual 110.70 93.80 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 127.24 -12.84 2.30e+00 1.89e-01 3.12e+01 angle pdb=" C LEU A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 ... (remaining 21808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 9516 23.18 - 46.36: 774 46.36 - 69.54: 161 69.54 - 92.72: 41 92.72 - 115.90: 4 Dihedral angle restraints: 10496 sinusoidal: 5033 harmonic: 5463 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 151.54 -58.54 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.74 57.74 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual -86.00 -137.05 51.05 1 1.00e+01 1.00e-02 3.56e+01 ... (remaining 10493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 2553 0.154 - 0.307: 79 0.307 - 0.461: 4 0.461 - 0.614: 0 0.614 - 0.768: 1 Chirality restraints: 2637 Sorted by residual: chirality pdb=" CB ILE B 294 " pdb=" CA ILE B 294 " pdb=" CG1 ILE B 294 " pdb=" CG2 ILE B 294 " both_signs ideal model delta sigma weight residual False 2.64 1.88 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C1 NAG A 709 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 709 " pdb=" O5 NAG A 709 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASN B 80 " pdb=" N ASN B 80 " pdb=" C ASN B 80 " pdb=" CB ASN B 80 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2634 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 712 " 0.178 2.00e-02 2.50e+03 1.50e-01 2.80e+02 pdb=" C7 NAG C 712 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG C 712 " 0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 712 " -0.248 2.00e-02 2.50e+03 pdb=" O7 NAG C 712 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 419 " -0.668 9.50e-02 1.11e+02 3.01e-01 6.57e+01 pdb=" NE ARG B 419 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG B 419 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 419 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG B 419 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " 0.029 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN C 386 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG C 712 " 0.040 2.00e-02 2.50e+03 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 2 2.41 - 3.04: 8772 3.04 - 3.66: 22514 3.66 - 4.28: 34260 4.28 - 4.90: 57356 Nonbonded interactions: 122904 Sorted by model distance: nonbonded pdb=" OD1 ASN C 651 " pdb=" NZ LYS C 655 " model vdw 1.792 3.120 nonbonded pdb=" O ASN B 651 " pdb=" CG LYS B 655 " model vdw 1.956 3.440 nonbonded pdb=" O5 MAN E 4 " pdb=" O6 MAN E 4 " model vdw 2.452 2.432 nonbonded pdb=" OD1 ASN C 651 " pdb=" CE LYS C 655 " model vdw 2.454 3.440 nonbonded pdb=" O5 MAN M 4 " pdb=" O6 MAN M 4 " model vdw 2.473 2.432 ... (remaining 122899 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 36 through 56 or resid 66 through 135 or resid 150 through \ 457 or resid 463 through 501 or resid 522 through 546 or resid 569 through 710) \ ) selection = (chain 'B' and (resid 36 through 457 or resid 460 through 501 or resid 522 throu \ gh 710)) selection = (chain 'C' and (resid 36 through 56 or resid 66 through 135 or resid 150 through \ 457 or resid 463 through 501 or resid 522 through 546 or resid 569 through 710) \ ) } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.610 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16171 Z= 0.297 Angle : 1.276 16.901 22072 Z= 0.655 Chirality : 0.069 0.768 2637 Planarity : 0.010 0.301 2699 Dihedral : 17.018 115.900 6859 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.42 % Allowed : 22.50 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 1848 helix: 0.46 (0.26), residues: 375 sheet: -0.59 (0.21), residues: 524 loop : -1.03 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.002 ARG B 419 TYR 0.018 0.002 TYR B 173 PHE 0.030 0.002 PHE C 233 TRP 0.063 0.003 TRP A 631 HIS 0.014 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.30 (16073) covalent geometry : angle 1.23825 / 0.65 (21813) SS BOND : bond 0.00677 / 0.45 ( 35) SS BOND : angle 3.24223 / 2.37 ( 70) hydrogen bonds : bond 0.13655 / 8.69 ( 435) hydrogen bonds : angle 6.88309 / 4.84 ( 1194) link_ALPHA1-2 : bond 0.00824 / 0.43 ( 1) link_ALPHA1-2 : angle 1.59244 / 0.87 ( 3) link_ALPHA1-3 : bond 0.00694 / 0.36 ( 3) link_ALPHA1-3 : angle 1.30234 / 0.82 ( 9) link_BETA1-4 : bond 0.00782 / 0.41 ( 16) link_BETA1-4 : angle 2.95133 / 1.98 ( 48) link_NAG-ASN : bond 0.00769 / 0.54 ( 43) link_NAG-ASN : angle 3.22569 / 2.14 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 325 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7355 (mp0) cc_final: 0.7103 (mt-10) REVERT: B 104 MET cc_start: 0.8427 (ttt) cc_final: 0.8099 (ttt) REVERT: B 207 LYS cc_start: 0.7923 (tptt) cc_final: 0.7680 (tptt) REVERT: B 377 ASN cc_start: 0.8233 (p0) cc_final: 0.7981 (p0) REVERT: C 95 MET cc_start: 0.7353 (ptm) cc_final: 0.6938 (ptm) REVERT: C 231 LYS cc_start: 0.7390 (mmtt) cc_final: 0.6885 (mmtt) REVERT: C 542 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8214 (ttp-170) REVERT: C 588 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7543 (mtt-85) REVERT: C 646 LEU cc_start: 0.7734 (tp) cc_final: 0.7414 (pp) REVERT: H 77 GLN cc_start: 0.7914 (mt0) cc_final: 0.7655 (mt0) REVERT: L 56 ASP cc_start: 0.8449 (m-30) cc_final: 0.8245 (m-30) outliers start: 7 outliers final: 5 residues processed: 331 average time/residue: 0.1273 time to fit residues: 63.8924 Evaluate side-chains 216 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain L residue 91 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 72 HIS B 99 ASN B 103 GLN B 287 GLN B 652 GLN C 330 HIS C 374 HIS C 650 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.159320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133280 restraints weight = 24446.766| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.79 r_work: 0.3497 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16171 Z= 0.160 Angle : 0.737 9.974 22072 Z= 0.355 Chirality : 0.050 0.428 2637 Planarity : 0.004 0.058 2699 Dihedral : 9.907 106.517 3326 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.25 % Allowed : 22.08 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.52 (0.19), residues: 1848 helix: 1.18 (0.26), residues: 371 sheet: -0.42 (0.21), residues: 542 loop : -0.89 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 588 TYR 0.013 0.002 TYR A 173 PHE 0.026 0.002 PHE B 522 TRP 0.034 0.002 TRP A 35 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (16073) covalent geometry : angle 0.69616 / 0.35 (21813) SS BOND : bond 0.00366 / 0.24 ( 35) SS BOND : angle 1.41973 / 1.00 ( 70) hydrogen bonds : bond 0.04194 / 2.83 ( 435) hydrogen bonds : angle 5.54306 / 3.90 ( 1194) link_ALPHA1-2 : bond 0.00736 / 0.39 ( 1) link_ALPHA1-2 : angle 1.49559 / 0.84 ( 3) link_ALPHA1-3 : bond 0.00956 / 0.48 ( 3) link_ALPHA1-3 : angle 1.45744 / 0.91 ( 9) link_BETA1-4 : bond 0.00473 / 0.22 ( 16) link_BETA1-4 : angle 2.55555 / 1.72 ( 48) link_NAG-ASN : bond 0.00433 / 0.33 ( 43) link_NAG-ASN : angle 2.67718 / 1.80 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7611 (mp0) cc_final: 0.7135 (mt-10) REVERT: A 104 MET cc_start: 0.8458 (ttt) cc_final: 0.8194 (ttt) REVERT: A 129 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8986 (mt) REVERT: A 244 THR cc_start: 0.5795 (OUTLIER) cc_final: 0.5534 (t) REVERT: A 621 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7301 (mt-10) REVERT: A 652 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7198 (tt0) REVERT: B 377 ASN cc_start: 0.8313 (p0) cc_final: 0.8086 (p0) REVERT: B 530 MET cc_start: 0.7323 (tpp) cc_final: 0.6318 (mmt) REVERT: C 95 MET cc_start: 0.7415 (ptm) cc_final: 0.6984 (ptm) REVERT: C 141 ASP cc_start: 0.6304 (OUTLIER) cc_final: 0.5932 (p0) REVERT: C 530 MET cc_start: 0.7821 (mmm) cc_final: 0.7345 (mmt) REVERT: C 542 ARG cc_start: 0.8429 (ttm170) cc_final: 0.8187 (ttp-170) REVERT: C 588 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7708 (mtt-85) REVERT: C 590 GLN cc_start: 0.7932 (tp40) cc_final: 0.7506 (tm-30) REVERT: C 595 ILE cc_start: 0.8553 (mt) cc_final: 0.8307 (mm) REVERT: C 646 LEU cc_start: 0.7920 (tp) cc_final: 0.7561 (pp) REVERT: H 77 GLN cc_start: 0.8028 (mt0) cc_final: 0.7707 (mt0) REVERT: H 82 ARG cc_start: 0.8345 (mtm110) cc_final: 0.8115 (mtm-85) outliers start: 71 outliers final: 44 residues processed: 279 average time/residue: 0.1170 time to fit residues: 51.0694 Evaluate side-chains 241 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 46 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 640 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127947 restraints weight = 24742.003| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.10 r_work: 0.3397 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16171 Z= 0.227 Angle : 0.748 10.547 22072 Z= 0.363 Chirality : 0.051 0.386 2637 Planarity : 0.004 0.058 2699 Dihedral : 9.599 107.669 3326 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.57 % Allowed : 22.50 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.63 (0.19), residues: 1848 helix: 1.05 (0.26), residues: 372 sheet: -0.46 (0.21), residues: 527 loop : -0.95 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.016 0.002 TYR B 484 PHE 0.020 0.002 PHE B 522 TRP 0.022 0.002 TRP A 35 HIS 0.007 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (16073) covalent geometry : angle 0.70918 / 0.35 (21813) SS BOND : bond 0.00545 / 0.36 ( 35) SS BOND : angle 1.65181 / 1.18 ( 70) hydrogen bonds : bond 0.04118 / 2.80 ( 435) hydrogen bonds : angle 5.36377 / 3.78 ( 1194) link_ALPHA1-2 : bond 0.00510 / 0.27 ( 1) link_ALPHA1-2 : angle 1.73896 / 0.97 ( 3) link_ALPHA1-3 : bond 0.01126 / 0.58 ( 3) link_ALPHA1-3 : angle 1.44386 / 0.92 ( 9) link_BETA1-4 : bond 0.00334 / 0.19 ( 16) link_BETA1-4 : angle 2.50820 / 1.69 ( 48) link_NAG-ASN : bond 0.00434 / 0.34 ( 43) link_NAG-ASN : angle 2.57028 / 1.73 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6474 (mtm) cc_final: 0.5803 (ptt) REVERT: A 97 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8296 (ttpp) REVERT: A 104 MET cc_start: 0.8699 (ttt) cc_final: 0.8382 (ttt) REVERT: A 491 ILE cc_start: 0.8329 (mm) cc_final: 0.8034 (mm) REVERT: C 95 MET cc_start: 0.7452 (ptm) cc_final: 0.6960 (ptm) REVERT: C 305 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8296 (ttmm) REVERT: C 530 MET cc_start: 0.7737 (mmm) cc_final: 0.7010 (mtt) REVERT: C 542 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8323 (ttp-170) REVERT: C 588 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7773 (mtt-85) REVERT: C 590 GLN cc_start: 0.7913 (tp40) cc_final: 0.7508 (tm-30) REVERT: C 595 ILE cc_start: 0.8620 (mt) cc_final: 0.8366 (mm) outliers start: 93 outliers final: 63 residues processed: 272 average time/residue: 0.1165 time to fit residues: 49.1667 Evaluate side-chains 249 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 152 optimal weight: 0.0170 chunk 160 optimal weight: 0.0040 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 543 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130738 restraints weight = 24459.051| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.82 r_work: 0.3464 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16171 Z= 0.120 Angle : 0.644 9.524 22072 Z= 0.310 Chirality : 0.047 0.345 2637 Planarity : 0.004 0.058 2699 Dihedral : 8.944 108.805 3324 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.43 % Allowed : 24.30 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 1848 helix: 1.24 (0.26), residues: 380 sheet: -0.32 (0.21), residues: 534 loop : -0.83 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.016 0.001 TYR A 173 PHE 0.024 0.001 PHE C 233 TRP 0.015 0.001 TRP A 35 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16073) covalent geometry : angle 0.60942 / 0.30 (21813) SS BOND : bond 0.00319 / 0.21 ( 35) SS BOND : angle 1.28743 / 0.92 ( 70) hydrogen bonds : bond 0.03524 / 2.42 ( 435) hydrogen bonds : angle 5.02432 / 3.52 ( 1194) link_ALPHA1-2 : bond 0.00726 / 0.38 ( 1) link_ALPHA1-2 : angle 1.44819 / 0.81 ( 3) link_ALPHA1-3 : bond 0.01056 / 0.53 ( 3) link_ALPHA1-3 : angle 1.25756 / 0.78 ( 9) link_BETA1-4 : bond 0.00404 / 0.21 ( 16) link_BETA1-4 : angle 2.14890 / 1.44 ( 48) link_NAG-ASN : bond 0.00383 / 0.30 ( 43) link_NAG-ASN : angle 2.34176 / 1.57 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6259 (mtm) cc_final: 0.5751 (ptt) REVERT: A 97 LYS cc_start: 0.8471 (ttmm) cc_final: 0.8208 (ttpp) REVERT: A 104 MET cc_start: 0.8559 (ttt) cc_final: 0.8279 (ttt) REVERT: A 284 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 247 CYS cc_start: 0.5638 (m) cc_final: 0.5264 (m) REVERT: B 475 MET cc_start: 0.8530 (tpp) cc_final: 0.8085 (mmm) REVERT: B 530 MET cc_start: 0.7457 (tpp) cc_final: 0.6392 (mmt) REVERT: C 39 TYR cc_start: 0.7879 (m-80) cc_final: 0.7483 (m-80) REVERT: C 95 MET cc_start: 0.7397 (ptm) cc_final: 0.6920 (ptm) REVERT: C 530 MET cc_start: 0.7628 (mmm) cc_final: 0.7017 (mtt) REVERT: C 542 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8255 (ttp-170) REVERT: C 588 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7665 (mtt-85) REVERT: C 590 GLN cc_start: 0.7897 (tp40) cc_final: 0.7483 (tm-30) REVERT: C 595 ILE cc_start: 0.8567 (mt) cc_final: 0.8321 (mm) outliers start: 74 outliers final: 51 residues processed: 259 average time/residue: 0.1092 time to fit residues: 44.0057 Evaluate side-chains 238 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 91 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 151 optimal weight: 0.0270 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 0.0040 chunk 185 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.153624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127883 restraints weight = 24628.114| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.88 r_work: 0.3414 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16171 Z= 0.187 Angle : 0.685 9.619 22072 Z= 0.330 Chirality : 0.048 0.345 2637 Planarity : 0.004 0.055 2699 Dihedral : 8.926 107.501 3324 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.51 % Allowed : 23.52 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.19), residues: 1848 helix: 1.18 (0.27), residues: 383 sheet: -0.30 (0.22), residues: 516 loop : -0.83 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 588 TYR 0.014 0.002 TYR B 484 PHE 0.012 0.002 PHE A 233 TRP 0.015 0.002 TRP A 479 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (16073) covalent geometry : angle 0.65030 / 0.32 (21813) SS BOND : bond 0.00425 / 0.29 ( 35) SS BOND : angle 1.33791 / 0.95 ( 70) hydrogen bonds : bond 0.03644 / 2.48 ( 435) hydrogen bonds : angle 5.03281 / 3.56 ( 1194) link_ALPHA1-2 : bond 0.00506 / 0.27 ( 1) link_ALPHA1-2 : angle 1.67561 / 0.94 ( 3) link_ALPHA1-3 : bond 0.01073 / 0.55 ( 3) link_ALPHA1-3 : angle 1.32565 / 0.84 ( 9) link_BETA1-4 : bond 0.00335 / 0.18 ( 16) link_BETA1-4 : angle 2.29873 / 1.55 ( 48) link_NAG-ASN : bond 0.00438 / 0.35 ( 43) link_NAG-ASN : angle 2.37099 / 1.58 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 191 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6415 (mtm) cc_final: 0.5860 (ptt) REVERT: A 104 MET cc_start: 0.8637 (ttt) cc_final: 0.8322 (ttt) REVERT: A 161 MET cc_start: 0.8579 (tpp) cc_final: 0.8325 (ttp) REVERT: A 284 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7650 (mp) REVERT: A 500 ARG cc_start: 0.5674 (mmt180) cc_final: 0.5132 (ptt90) REVERT: B 575 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: B 643 TYR cc_start: 0.7587 (m-10) cc_final: 0.7322 (m-80) REVERT: B 650 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6602 (mt0) REVERT: C 39 TYR cc_start: 0.8033 (m-80) cc_final: 0.7621 (m-80) REVERT: C 95 MET cc_start: 0.7501 (ptm) cc_final: 0.6977 (ptm) REVERT: C 153 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: C 192 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7744 (ptt-90) REVERT: C 530 MET cc_start: 0.7590 (mmm) cc_final: 0.7167 (mtt) REVERT: C 542 ARG cc_start: 0.8567 (ttm170) cc_final: 0.8360 (ttp-170) REVERT: C 590 GLN cc_start: 0.7842 (tp40) cc_final: 0.7473 (tm-30) REVERT: C 595 ILE cc_start: 0.8634 (mt) cc_final: 0.8387 (mm) outliers start: 92 outliers final: 67 residues processed: 261 average time/residue: 0.1129 time to fit residues: 45.5015 Evaluate side-chains 254 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 160 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.0070 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 0.2980 chunk 127 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 182 optimal weight: 0.0060 chunk 140 optimal weight: 1.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 258 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131902 restraints weight = 24345.345| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.00 r_work: 0.3462 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16171 Z= 0.111 Angle : 0.628 9.522 22072 Z= 0.302 Chirality : 0.046 0.322 2637 Planarity : 0.004 0.055 2699 Dihedral : 8.553 108.901 3324 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.31 % Allowed : 25.01 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.19), residues: 1848 helix: 1.33 (0.27), residues: 382 sheet: -0.19 (0.21), residues: 541 loop : -0.82 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 588 TYR 0.014 0.001 TYR H 100G PHE 0.026 0.001 PHE C 233 TRP 0.014 0.001 TRP H 103 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16073) covalent geometry : angle 0.59535 / 0.29 (21813) SS BOND : bond 0.00301 / 0.21 ( 35) SS BOND : angle 1.36911 / 0.96 ( 70) hydrogen bonds : bond 0.03334 / 2.27 ( 435) hydrogen bonds : angle 4.85662 / 3.43 ( 1194) link_ALPHA1-2 : bond 0.00734 / 0.39 ( 1) link_ALPHA1-2 : angle 1.42841 / 0.80 ( 3) link_ALPHA1-3 : bond 0.00969 / 0.49 ( 3) link_ALPHA1-3 : angle 1.20434 / 0.74 ( 9) link_BETA1-4 : bond 0.00401 / 0.21 ( 16) link_BETA1-4 : angle 1.99096 / 1.34 ( 48) link_NAG-ASN : bond 0.00371 / 0.28 ( 43) link_NAG-ASN : angle 2.21677 / 1.48 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6271 (mtm) cc_final: 0.5851 (ptt) REVERT: A 104 MET cc_start: 0.8570 (ttt) cc_final: 0.8364 (ttt) REVERT: A 284 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7658 (mp) REVERT: A 426 MET cc_start: 0.8046 (ttm) cc_final: 0.7744 (ttp) REVERT: A 500 ARG cc_start: 0.5764 (mmt180) cc_final: 0.5183 (ptt90) REVERT: B 247 CYS cc_start: 0.5672 (m) cc_final: 0.5325 (m) REVERT: B 475 MET cc_start: 0.8494 (tpp) cc_final: 0.8134 (mmm) REVERT: B 643 TYR cc_start: 0.7567 (m-10) cc_final: 0.7299 (m-80) REVERT: C 39 TYR cc_start: 0.7996 (m-80) cc_final: 0.7511 (m-80) REVERT: C 95 MET cc_start: 0.7417 (ptm) cc_final: 0.6904 (ptm) REVERT: C 153 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: C 233 PHE cc_start: 0.7657 (t80) cc_final: 0.7445 (t80) REVERT: C 305 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: C 530 MET cc_start: 0.7536 (mmm) cc_final: 0.7236 (mtt) REVERT: C 542 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8338 (ttp-170) REVERT: C 588 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7673 (mtt-85) REVERT: C 590 GLN cc_start: 0.7811 (tp40) cc_final: 0.7520 (tm-30) REVERT: C 595 ILE cc_start: 0.8574 (mt) cc_final: 0.8325 (mm) outliers start: 72 outliers final: 53 residues processed: 260 average time/residue: 0.1159 time to fit residues: 47.1248 Evaluate side-chains 248 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 87 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 136 optimal weight: 0.0270 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128883 restraints weight = 24360.523| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.02 r_work: 0.3431 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16171 Z= 0.155 Angle : 0.650 9.600 22072 Z= 0.312 Chirality : 0.047 0.328 2637 Planarity : 0.004 0.044 2699 Dihedral : 8.573 107.989 3324 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.39 % Allowed : 24.12 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1848 helix: 1.27 (0.27), residues: 383 sheet: -0.17 (0.22), residues: 523 loop : -0.83 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 588 TYR 0.015 0.001 TYR H 100G PHE 0.024 0.001 PHE C 233 TRP 0.022 0.001 TRP A 631 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (16073) covalent geometry : angle 0.61748 / 0.30 (21813) SS BOND : bond 0.00362 / 0.25 ( 35) SS BOND : angle 1.32574 / 0.94 ( 70) hydrogen bonds : bond 0.03456 / 2.36 ( 435) hydrogen bonds : angle 4.91548 / 3.48 ( 1194) link_ALPHA1-2 : bond 0.00569 / 0.30 ( 1) link_ALPHA1-2 : angle 1.60443 / 0.90 ( 3) link_ALPHA1-3 : bond 0.00937 / 0.47 ( 3) link_ALPHA1-3 : angle 1.29851 / 0.82 ( 9) link_BETA1-4 : bond 0.00346 / 0.18 ( 16) link_BETA1-4 : angle 2.13250 / 1.44 ( 48) link_NAG-ASN : bond 0.00387 / 0.31 ( 43) link_NAG-ASN : angle 2.24198 / 1.49 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 196 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.6380 (mtm) cc_final: 0.5835 (ptt) REVERT: A 104 MET cc_start: 0.8620 (ttt) cc_final: 0.8373 (ttt) REVERT: A 284 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7649 (mp) REVERT: A 434 MET cc_start: 0.8454 (ptm) cc_final: 0.8119 (ptm) REVERT: A 500 ARG cc_start: 0.5576 (mmt180) cc_final: 0.5033 (ptt90) REVERT: B 247 CYS cc_start: 0.5638 (m) cc_final: 0.5285 (m) REVERT: B 575 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 95 MET cc_start: 0.7486 (ptm) cc_final: 0.6948 (ptm) REVERT: C 129 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (mt) REVERT: C 153 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: C 192 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7745 (ptt-90) REVERT: C 233 PHE cc_start: 0.7796 (t80) cc_final: 0.7566 (t80) REVERT: C 305 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8213 (ttmm) REVERT: C 530 MET cc_start: 0.7603 (mmm) cc_final: 0.7200 (mtt) REVERT: C 542 ARG cc_start: 0.8590 (ttm170) cc_final: 0.8375 (ttp-170) REVERT: C 590 GLN cc_start: 0.7900 (tp40) cc_final: 0.7521 (tm-30) REVERT: C 595 ILE cc_start: 0.8595 (mt) cc_final: 0.8328 (mm) outliers start: 90 outliers final: 67 residues processed: 267 average time/residue: 0.1104 time to fit residues: 45.2955 Evaluate side-chains 259 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 186 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 140 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN L 27 HIS ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130983 restraints weight = 24559.839| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.00 r_work: 0.3451 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16171 Z= 0.125 Angle : 0.633 9.563 22072 Z= 0.304 Chirality : 0.046 0.313 2637 Planarity : 0.004 0.043 2699 Dihedral : 8.378 108.924 3324 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.49 % Allowed : 24.60 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1848 helix: 1.33 (0.27), residues: 383 sheet: -0.14 (0.22), residues: 528 loop : -0.84 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.015 0.001 TYR H 100G PHE 0.023 0.001 PHE C 233 TRP 0.020 0.001 TRP A 631 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16073) covalent geometry : angle 0.60236 / 0.30 (21813) SS BOND : bond 0.00361 / 0.24 ( 35) SS BOND : angle 1.34932 / 0.95 ( 70) hydrogen bonds : bond 0.03315 / 2.27 ( 435) hydrogen bonds : angle 4.86835 / 3.46 ( 1194) link_ALPHA1-2 : bond 0.00683 / 0.36 ( 1) link_ALPHA1-2 : angle 1.46420 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00924 / 0.47 ( 3) link_ALPHA1-3 : angle 1.22445 / 0.76 ( 9) link_BETA1-4 : bond 0.00380 / 0.20 ( 16) link_BETA1-4 : angle 1.98253 / 1.35 ( 48) link_NAG-ASN : bond 0.00352 / 0.27 ( 43) link_NAG-ASN : angle 2.15851 / 1.44 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7635 (mp) REVERT: A 500 ARG cc_start: 0.5943 (mmt180) cc_final: 0.5403 (ptt90) REVERT: B 207 LYS cc_start: 0.7750 (tmtt) cc_final: 0.7505 (tmtt) REVERT: B 247 CYS cc_start: 0.5549 (m) cc_final: 0.5231 (m) REVERT: B 475 MET cc_start: 0.8532 (tpp) cc_final: 0.8198 (mmm) REVERT: B 575 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: C 95 MET cc_start: 0.7485 (ptm) cc_final: 0.6959 (ptm) REVERT: C 129 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (mt) REVERT: C 153 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: C 305 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8154 (ttmm) REVERT: C 530 MET cc_start: 0.7586 (mmm) cc_final: 0.7162 (mtt) REVERT: C 588 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7681 (mtt-85) REVERT: C 590 GLN cc_start: 0.7825 (tp40) cc_final: 0.7514 (tm-30) REVERT: C 595 ILE cc_start: 0.8525 (mt) cc_final: 0.8275 (mm) outliers start: 75 outliers final: 62 residues processed: 252 average time/residue: 0.1081 time to fit residues: 41.9906 Evaluate side-chains 254 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 134 optimal weight: 0.3980 chunk 113 optimal weight: 0.4980 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131829 restraints weight = 24480.904| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.96 r_work: 0.3460 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16171 Z= 0.120 Angle : 0.622 9.571 22072 Z= 0.298 Chirality : 0.046 0.311 2637 Planarity : 0.004 0.045 2699 Dihedral : 8.230 108.449 3324 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.19 % Allowed : 24.96 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1848 helix: 1.33 (0.27), residues: 383 sheet: -0.06 (0.22), residues: 532 loop : -0.81 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.017 0.001 TYR B 643 PHE 0.014 0.001 PHE A 233 TRP 0.020 0.001 TRP A 631 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16073) covalent geometry : angle 0.59143 / 0.29 (21813) SS BOND : bond 0.00343 / 0.23 ( 35) SS BOND : angle 1.32017 / 0.92 ( 70) hydrogen bonds : bond 0.03264 / 2.24 ( 435) hydrogen bonds : angle 4.81117 / 3.42 ( 1194) link_ALPHA1-2 : bond 0.00687 / 0.36 ( 1) link_ALPHA1-2 : angle 1.46525 / 0.81 ( 3) link_ALPHA1-3 : bond 0.00903 / 0.45 ( 3) link_ALPHA1-3 : angle 1.23548 / 0.76 ( 9) link_BETA1-4 : bond 0.00379 / 0.20 ( 16) link_BETA1-4 : angle 1.93829 / 1.31 ( 48) link_NAG-ASN : bond 0.00348 / 0.27 ( 43) link_NAG-ASN : angle 2.11247 / 1.40 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 199 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7626 (mp) REVERT: A 500 ARG cc_start: 0.5925 (mmt180) cc_final: 0.5384 (ptt90) REVERT: B 207 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7397 (tmtt) REVERT: B 247 CYS cc_start: 0.5710 (m) cc_final: 0.5407 (m) REVERT: B 475 MET cc_start: 0.8492 (tpp) cc_final: 0.8198 (mmm) REVERT: B 575 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: C 95 MET cc_start: 0.7485 (ptm) cc_final: 0.6947 (ptm) REVERT: C 129 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8617 (mt) REVERT: C 153 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: C 305 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8139 (ttmm) REVERT: C 530 MET cc_start: 0.7632 (mmm) cc_final: 0.7116 (mtt) REVERT: C 588 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7646 (mtt-85) REVERT: C 590 GLN cc_start: 0.7827 (tp40) cc_final: 0.7495 (tm-30) REVERT: C 595 ILE cc_start: 0.8458 (mt) cc_final: 0.8195 (mm) REVERT: C 623 TRP cc_start: 0.6168 (m100) cc_final: 0.5881 (m100) outliers start: 70 outliers final: 60 residues processed: 254 average time/residue: 0.1158 time to fit residues: 45.2715 Evaluate side-chains 258 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 46 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.155661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129635 restraints weight = 24522.994| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.07 r_work: 0.3424 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16171 Z= 0.148 Angle : 0.648 9.593 22072 Z= 0.311 Chirality : 0.047 0.313 2637 Planarity : 0.004 0.043 2699 Dihedral : 8.286 108.394 3324 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.49 % Allowed : 24.90 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1848 helix: 1.28 (0.27), residues: 382 sheet: -0.06 (0.22), residues: 529 loop : -0.83 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.023 0.001 TYR C 643 PHE 0.013 0.001 PHE A 233 TRP 0.022 0.001 TRP B 96 HIS 0.006 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16073) covalent geometry : angle 0.61667 / 0.30 (21813) SS BOND : bond 0.00377 / 0.26 ( 35) SS BOND : angle 1.33854 / 0.95 ( 70) hydrogen bonds : bond 0.03383 / 2.31 ( 435) hydrogen bonds : angle 4.87747 / 3.46 ( 1194) link_ALPHA1-2 : bond 0.00589 / 0.31 ( 1) link_ALPHA1-2 : angle 1.55937 / 0.87 ( 3) link_ALPHA1-3 : bond 0.00874 / 0.44 ( 3) link_ALPHA1-3 : angle 1.25360 / 0.78 ( 9) link_BETA1-4 : bond 0.00373 / 0.19 ( 16) link_BETA1-4 : angle 2.16640 / 1.44 ( 48) link_NAG-ASN : bond 0.00356 / 0.28 ( 43) link_NAG-ASN : angle 2.13548 / 1.41 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7629 (mp) REVERT: A 500 ARG cc_start: 0.5882 (mmt180) cc_final: 0.5348 (ptt90) REVERT: B 207 LYS cc_start: 0.7753 (tmtt) cc_final: 0.7327 (tptt) REVERT: B 247 CYS cc_start: 0.5734 (m) cc_final: 0.5442 (m) REVERT: B 575 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 95 MET cc_start: 0.7532 (ptm) cc_final: 0.6976 (ptm) REVERT: C 129 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8615 (mt) REVERT: C 153 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: C 192 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7717 (ptt-90) REVERT: C 305 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8161 (ttmm) REVERT: C 530 MET cc_start: 0.7544 (mmm) cc_final: 0.7167 (mtt) REVERT: C 588 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7647 (mtt-85) REVERT: C 590 GLN cc_start: 0.7858 (tp40) cc_final: 0.7500 (tm-30) REVERT: C 595 ILE cc_start: 0.8464 (mt) cc_final: 0.8199 (mm) outliers start: 75 outliers final: 65 residues processed: 248 average time/residue: 0.0990 time to fit residues: 38.2348 Evaluate side-chains 256 residues out of total 1671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 185 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 352 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 91 HIS Chi-restraints excluded: chain L residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 48 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.130158 restraints weight = 24387.034| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.90 r_work: 0.3449 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16171 Z= 0.130 Angle : 0.630 9.579 22072 Z= 0.301 Chirality : 0.046 0.307 2637 Planarity : 0.004 0.043 2699 Dihedral : 8.182 109.071 3324 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.43 % Allowed : 24.90 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.20), residues: 1848 helix: 1.31 (0.27), residues: 382 sheet: -0.05 (0.23), residues: 529 loop : -0.82 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 588 TYR 0.026 0.001 TYR B 643 PHE 0.014 0.001 PHE A 233 TRP 0.020 0.001 TRP A 631 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16073) covalent geometry : angle 0.60050 / 0.29 (21813) SS BOND : bond 0.00341 / 0.23 ( 35) SS BOND : angle 1.26739 / 0.90 ( 70) hydrogen bonds : bond 0.03307 / 2.27 ( 435) hydrogen bonds : angle 4.83203 / 3.42 ( 1194) link_ALPHA1-2 : bond 0.00667 / 0.35 ( 1) link_ALPHA1-2 : angle 1.48001 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00870 / 0.44 ( 3) link_ALPHA1-3 : angle 1.23993 / 0.77 ( 9) link_BETA1-4 : bond 0.00379 / 0.20 ( 16) link_BETA1-4 : angle 2.03040 / 1.36 ( 48) link_NAG-ASN : bond 0.00344 / 0.26 ( 43) link_NAG-ASN : angle 2.09940 / 1.39 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.93 seconds wall clock time: 62 minutes 34.00 seconds (3754.00 seconds total)