Starting phenix.real_space_refine on Thu Aug 6 00:16:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0b_37973/08_2026/8x0b_37973.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 5 Type Number sf(0) Gaussians S 118 5.16 5 C 7964 2.51 5 N 2056 2.21 5 O 2275 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12415 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6140 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 33, 'TRANS': 746} Chain breaks: 1 Chain: "B" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6140 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 33, 'TRANS': 746} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 2.76, per 1000 atoms: 0.22 Number of scatterers: 12415 At special positions: 0 Unit cell: (103.32, 83.16, 183.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 118 16.00 F 2 9.00 O 2275 8.00 N 2056 7.00 C 7964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.08 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.04 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.02 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.04 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.02 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.06 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.04 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " 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 NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 577.3 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 16 sheets defined 47.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.735A pdb=" N GLU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.674A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.523A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.855A pdb=" N GLU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.803A pdb=" N ALA A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.794A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 396 through 419 removed outlier: 4.081A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 602 Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.675A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 675 removed outlier: 3.642A pdb=" N LEU A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.518A pdb=" N TYR A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 715 removed outlier: 3.626A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 762 removed outlier: 3.556A pdb=" N VAL A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 769 through 788 removed outlier: 3.529A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 797 through 817 Processing helix chain 'A' and resid 818 through 824 removed outlier: 3.608A pdb=" N TYR A 823 " --> pdb=" O VAL A 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.802A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.721A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.507A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.566A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.881A pdb=" N GLU B 238 " --> pdb=" O MET B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.760A pdb=" N ALA B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 3.794A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.749A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.501A pdb=" N THR B 563 " --> pdb=" O ASP B 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.783A pdb=" N ILE B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 634 removed outlier: 5.441A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 679 removed outlier: 3.596A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.276A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 673 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 715 removed outlier: 4.446A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 762 removed outlier: 3.757A pdb=" N ALA B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 769 through 788 removed outlier: 4.407A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 removed outlier: 4.377A pdb=" N GLY B 794 " --> pdb=" O PRO B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 815 Processing helix chain 'B' and resid 817 through 824 removed outlier: 4.240A pdb=" N LYS B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.044A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.291A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329 removed outlier: 6.743A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.898A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.352A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN B 169 " --> pdb=" O MET B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 248 removed outlier: 8.026A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.738A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB6, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AB7, first strand: chain 'B' and resid 719 through 720 551 hydrogen bonds defined for protein. 1608 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: 2.32 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2059 1.32 - 1.45: 3397 1.45 - 1.58: 7040 1.58 - 1.71: 0 1.71 - 1.84: 170 Bond restraints: 12666 Sorted by residual: bond pdb=" CA SER B 462 " pdb=" CB SER B 462 " ideal model delta sigma weight residual 1.537 1.501 0.036 1.38e-02 5.25e+03 6.88e+00 bond pdb=" CA SER B 795 " pdb=" CB SER B 795 " ideal model delta sigma weight residual 1.538 1.507 0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" CA SER A 462 " pdb=" CB SER A 462 " ideal model delta sigma weight residual 1.537 1.503 0.034 1.38e-02 5.25e+03 6.02e+00 bond pdb=" CA PRO A 685 " pdb=" CB PRO A 685 " ideal model delta sigma weight residual 1.531 1.546 -0.014 6.20e-03 2.60e+04 5.44e+00 bond pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta sigma weight residual 1.534 1.492 0.041 1.78e-02 3.16e+03 5.36e+00 ... (remaining 12661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 16316 2.07 - 4.15: 817 4.15 - 6.22: 20 6.22 - 8.30: 3 8.30 - 10.37: 2 Bond angle restraints: 17158 Sorted by residual: angle pdb=" N PRO A 716 " pdb=" CA PRO A 716 " pdb=" CB PRO A 716 " ideal model delta sigma weight residual 103.22 105.90 -2.68 5.20e-01 3.70e+00 2.65e+01 angle pdb=" N VAL A 819 " pdb=" CA VAL A 819 " pdb=" CB VAL A 819 " ideal model delta sigma weight residual 110.52 113.71 -3.19 6.70e-01 2.23e+00 2.26e+01 angle pdb=" N TYR B 619 " pdb=" CA TYR B 619 " pdb=" C TYR B 619 " ideal model delta sigma weight residual 113.18 107.93 5.25 1.33e+00 5.65e-01 1.56e+01 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 123.14 -10.37 3.00e+00 1.11e-01 1.19e+01 ... (remaining 17153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 7400 35.21 - 70.41: 234 70.41 - 105.62: 22 105.62 - 140.83: 3 140.83 - 176.04: 1 Dihedral angle restraints: 7660 sinusoidal: 3118 harmonic: 4542 Sorted by residual: dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 99 " pdb=" CB CYS A 99 " ideal model delta sinusoidal sigma weight residual -86.00 2.95 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B 644 " pdb=" SG CYS B 644 " pdb=" SG CYS B 733 " pdb=" CB CYS B 733 " ideal model delta sinusoidal sigma weight residual -86.00 -168.09 82.09 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 167.63 -74.63 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1582 0.093 - 0.187: 331 0.187 - 0.280: 5 0.280 - 0.374: 1 0.374 - 0.467: 1 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C2 XQT B 903 " pdb=" C1 XQT B 903 " pdb=" C3 XQT B 903 " pdb=" N1 XQT B 903 " both_signs ideal model delta sigma weight residual False 2.66 2.44 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1917 not shown) Planarity restraints: 2158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 XQT B 903 " 0.076 2.00e-02 2.50e+03 6.32e-02 5.00e+01 pdb=" C6 XQT B 903 " -0.029 2.00e-02 2.50e+03 pdb=" C7 XQT B 903 " 0.061 2.00e-02 2.50e+03 pdb=" N1 XQT B 903 " -0.098 2.00e-02 2.50e+03 pdb=" O2 XQT B 903 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 901 " -0.048 2.00e-02 2.50e+03 3.93e-02 1.93e+01 pdb=" C7 NAG B 901 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 901 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B 901 " 0.063 2.00e-02 2.50e+03 pdb=" O7 NAG B 901 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 XQT B 903 " -0.041 2.00e-02 2.50e+03 2.01e-02 9.07e+00 pdb=" C12 XQT B 903 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XQT B 903 " 0.023 2.00e-02 2.50e+03 pdb=" C14 XQT B 903 " 0.012 2.00e-02 2.50e+03 pdb=" C15 XQT B 903 " -0.002 2.00e-02 2.50e+03 pdb=" C16 XQT B 903 " -0.015 2.00e-02 2.50e+03 pdb=" C17 XQT B 903 " -0.009 2.00e-02 2.50e+03 pdb=" C18 XQT B 903 " 0.009 2.00e-02 2.50e+03 pdb=" F1 XQT B 903 " -0.005 2.00e-02 2.50e+03 ... (remaining 2155 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 476 2.71 - 3.26: 12762 3.26 - 3.81: 19984 3.81 - 4.35: 25918 4.35 - 4.90: 42142 Nonbonded interactions: 101282 Sorted by model distance: nonbonded pdb=" O TYR B 629 " pdb=" OG1 THR B 632 " model vdw 2.166 3.040 nonbonded pdb=" OE1 GLN B 519 " pdb=" O CYS B 537 " model vdw 2.201 3.040 nonbonded pdb=" O LYS A 263 " pdb=" OG SER A 266 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 331 " pdb=" O SER B 395 " model vdw 2.214 3.040 nonbonded pdb=" O ALA B 656 " pdb=" OG SER B 660 " model vdw 2.232 3.040 ... (remaining 101277 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 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 : 0.007 0.046 12688 Z= 0.450 Angle : 1.041 10.370 17204 Z= 0.701 Chirality : 0.066 0.467 1920 Planarity : 0.007 0.093 2156 Dihedral : 16.956 176.036 4688 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.60 % Favored : 91.88 % Rotamer: Outliers : 0.89 % Allowed : 19.29 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.20), residues: 1552 helix: 0.32 (0.19), residues: 693 sheet: -0.27 (0.41), residues: 155 loop : -2.28 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG A 668 TYR 0.031 0.004 TYR B 645 PHE 0.019 0.003 PHE A 544 TRP 0.018 0.005 TRP B 487 HIS 0.014 0.003 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.45 (12666) covalent geometry : angle 1.03795 / 0.70 (17158) SS BOND : bond 0.01361 / 0.82 ( 20) SS BOND : angle 1.68381 / 1.12 ( 40) hydrogen bonds : bond 0.15939 / 10.78 ( 551) hydrogen bonds : angle 5.53694 / 3.97 ( 1608) link_NAG-ASN : bond 0.00734 / 0.39 ( 2) link_NAG-ASN : angle 2.55269 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9313 (mmt) cc_final: 0.9059 (mmt) REVERT: A 693 GLN cc_start: 0.8535 (mp10) cc_final: 0.8211 (mp10) REVERT: A 779 TYR cc_start: 0.8786 (m-10) cc_final: 0.8343 (m-80) REVERT: A 817 MET cc_start: 0.8146 (mmm) cc_final: 0.7854 (mmm) REVERT: B 465 ARG cc_start: 0.9090 (ptp90) cc_final: 0.8880 (ptp90) outliers start: 12 outliers final: 5 residues processed: 162 average time/residue: 0.1084 time to fit residues: 25.8536 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 813 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0020 chunk 149 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070898 restraints weight = 28628.769| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.59 r_work: 0.2973 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12688 Z= 0.146 Angle : 0.616 9.146 17204 Z= 0.313 Chirality : 0.044 0.231 1920 Planarity : 0.004 0.047 2156 Dihedral : 9.526 97.713 1791 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 20.03 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1552 helix: 0.95 (0.20), residues: 692 sheet: -0.41 (0.42), residues: 160 loop : -1.88 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 25 TYR 0.013 0.001 TYR A 547 PHE 0.047 0.001 PHE A 776 TRP 0.014 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12666) covalent geometry : angle 0.61360 / 0.31 (17158) SS BOND : bond 0.00471 / 0.22 ( 20) SS BOND : angle 1.15565 / 0.74 ( 40) hydrogen bonds : bond 0.04762 / 3.19 ( 551) hydrogen bonds : angle 4.54615 / 3.26 ( 1608) link_NAG-ASN : bond 0.00379 / 0.20 ( 2) link_NAG-ASN : angle 2.01279 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 693 GLN cc_start: 0.8110 (mp10) cc_final: 0.7733 (mp10) REVERT: A 714 MET cc_start: 0.7364 (ptm) cc_final: 0.7162 (mtm) REVERT: A 776 PHE cc_start: 0.8922 (m-80) cc_final: 0.8676 (m-80) REVERT: A 779 TYR cc_start: 0.8765 (m-10) cc_final: 0.8226 (m-80) REVERT: B 31 MET cc_start: 0.8743 (mtp) cc_final: 0.8520 (ttp) REVERT: B 88 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (t0) REVERT: B 277 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8366 (t80) REVERT: B 429 MET cc_start: 0.7533 (ttt) cc_final: 0.7274 (ttt) outliers start: 40 outliers final: 14 residues processed: 173 average time/residue: 0.0945 time to fit residues: 25.0900 Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN B 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.103402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070537 restraints weight = 28867.812| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.43 r_work: 0.2984 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12688 Z= 0.154 Angle : 0.613 10.137 17204 Z= 0.305 Chirality : 0.044 0.229 1920 Planarity : 0.004 0.052 2156 Dihedral : 8.184 89.274 1783 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 3.56 % Allowed : 19.88 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.21), residues: 1552 helix: 1.10 (0.20), residues: 690 sheet: -0.41 (0.42), residues: 159 loop : -1.69 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.011 0.001 TYR B 659 PHE 0.037 0.001 PHE A 776 TRP 0.015 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (12666) covalent geometry : angle 0.61001 / 0.30 (17158) SS BOND : bond 0.00339 / 0.19 ( 20) SS BOND : angle 1.15095 / 0.72 ( 40) hydrogen bonds : bond 0.04355 / 2.91 ( 551) hydrogen bonds : angle 4.37268 / 3.12 ( 1608) link_NAG-ASN : bond 0.00347 / 0.17 ( 2) link_NAG-ASN : angle 2.34419 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.9345 (mmt) cc_final: 0.9084 (mmt) REVERT: A 693 GLN cc_start: 0.8078 (mp10) cc_final: 0.7684 (mp10) REVERT: A 722 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8134 (p0) REVERT: A 776 PHE cc_start: 0.8886 (m-80) cc_final: 0.8629 (m-80) REVERT: B 31 MET cc_start: 0.8717 (mtp) cc_final: 0.8509 (ttp) REVERT: B 88 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.7812 (t0) REVERT: B 277 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 720 MET cc_start: 0.7371 (mtt) cc_final: 0.7137 (mpp) outliers start: 48 outliers final: 27 residues processed: 179 average time/residue: 0.0913 time to fit residues: 25.6848 Evaluate side-chains 169 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 130 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 153 optimal weight: 0.2980 chunk 135 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 132 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.9052 > 50:) chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN B 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.103509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070606 restraints weight = 28858.719| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.43 r_work: 0.2980 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12688 Z= 0.140 Angle : 0.598 11.124 17204 Z= 0.297 Chirality : 0.043 0.227 1920 Planarity : 0.004 0.054 2156 Dihedral : 7.409 78.238 1783 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 4.23 % Allowed : 19.51 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1552 helix: 1.13 (0.20), residues: 692 sheet: -0.42 (0.42), residues: 159 loop : -1.65 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.015 0.001 TYR A 659 PHE 0.032 0.001 PHE A 776 TRP 0.014 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12666) covalent geometry : angle 0.59460 / 0.30 (17158) SS BOND : bond 0.00318 / 0.18 ( 20) SS BOND : angle 1.12849 / 0.71 ( 40) hydrogen bonds : bond 0.04086 / 2.75 ( 551) hydrogen bonds : angle 4.27969 / 3.06 ( 1608) link_NAG-ASN : bond 0.00374 / 0.18 ( 2) link_NAG-ASN : angle 2.63852 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 407 MET cc_start: 0.9028 (tpp) cc_final: 0.8617 (tpt) REVERT: A 416 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7508 (ttp) REVERT: A 442 MET cc_start: 0.9331 (mmt) cc_final: 0.9058 (mmt) REVERT: A 559 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 693 GLN cc_start: 0.8049 (mp10) cc_final: 0.7651 (mp10) REVERT: A 702 CYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7542 (p) REVERT: A 722 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 776 PHE cc_start: 0.8890 (m-80) cc_final: 0.8560 (m-80) REVERT: A 778 MET cc_start: 0.8652 (mmm) cc_final: 0.8389 (mmm) REVERT: A 779 TYR cc_start: 0.8760 (m-10) cc_final: 0.8258 (m-80) REVERT: B 31 MET cc_start: 0.8723 (mtp) cc_final: 0.8519 (ttp) REVERT: B 88 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 405 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8271 (m-10) REVERT: B 698 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6230 (t80) REVERT: B 711 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 768 PHE cc_start: 0.8322 (m-80) cc_final: 0.8119 (m-80) outliers start: 57 outliers final: 30 residues processed: 184 average time/residue: 0.0944 time to fit residues: 27.2125 Evaluate side-chains 178 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.103788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070845 restraints weight = 28841.951| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.46 r_work: 0.2984 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12688 Z= 0.126 Angle : 0.587 11.563 17204 Z= 0.290 Chirality : 0.042 0.222 1920 Planarity : 0.004 0.053 2156 Dihedral : 6.350 56.749 1783 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 4.08 % Allowed : 20.25 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1552 helix: 1.13 (0.20), residues: 692 sheet: -0.46 (0.42), residues: 159 loop : -1.66 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.030 0.001 TYR B 645 PHE 0.027 0.001 PHE A 776 TRP 0.014 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12666) covalent geometry : angle 0.58042 / 0.29 (17158) SS BOND : bond 0.00327 / 0.19 ( 20) SS BOND : angle 1.30779 / 0.84 ( 40) hydrogen bonds : bond 0.03915 / 2.63 ( 551) hydrogen bonds : angle 4.19297 / 2.99 ( 1608) link_NAG-ASN : bond 0.00407 / 0.19 ( 2) link_NAG-ASN : angle 3.80392 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 407 MET cc_start: 0.9030 (tpp) cc_final: 0.8639 (tpt) REVERT: A 416 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7522 (ttp) REVERT: A 442 MET cc_start: 0.9297 (mmt) cc_final: 0.9016 (mmt) REVERT: A 693 GLN cc_start: 0.8071 (mp10) cc_final: 0.7657 (mp10) REVERT: A 702 CYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7460 (p) REVERT: A 722 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8096 (p0) REVERT: A 776 PHE cc_start: 0.8878 (m-80) cc_final: 0.8535 (m-80) REVERT: A 779 TYR cc_start: 0.8759 (m-10) cc_final: 0.8253 (m-80) REVERT: B 31 MET cc_start: 0.8702 (mtp) cc_final: 0.8492 (ttp) REVERT: B 277 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 405 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: B 711 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8851 (mp) REVERT: B 768 PHE cc_start: 0.8310 (m-80) cc_final: 0.8087 (m-80) outliers start: 55 outliers final: 32 residues processed: 183 average time/residue: 0.0981 time to fit residues: 28.1142 Evaluate side-chains 177 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 63 optimal weight: 0.0770 chunk 85 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072148 restraints weight = 28897.478| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.44 r_work: 0.3030 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12688 Z= 0.107 Angle : 0.588 10.324 17204 Z= 0.287 Chirality : 0.043 0.254 1920 Planarity : 0.003 0.053 2156 Dihedral : 5.630 59.395 1782 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Rotamer: Outliers : 3.41 % Allowed : 21.44 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.22), residues: 1552 helix: 1.17 (0.20), residues: 689 sheet: -0.38 (0.43), residues: 154 loop : -1.55 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.030 0.001 TYR B 645 PHE 0.025 0.001 PHE A 776 TRP 0.013 0.001 TRP A 575 HIS 0.003 0.000 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (12666) covalent geometry : angle 0.58207 / 0.29 (17158) SS BOND : bond 0.00281 / 0.17 ( 20) SS BOND : angle 1.08569 / 0.70 ( 40) hydrogen bonds : bond 0.03654 / 2.44 ( 551) hydrogen bonds : angle 4.11494 / 2.93 ( 1608) link_NAG-ASN : bond 0.00413 / 0.20 ( 2) link_NAG-ASN : angle 3.78907 / 1.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 277 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8528 (t80) REVERT: A 407 MET cc_start: 0.9010 (tpp) cc_final: 0.8628 (tpt) REVERT: A 442 MET cc_start: 0.9299 (mmt) cc_final: 0.9078 (mmt) REVERT: A 559 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 693 GLN cc_start: 0.8100 (mp10) cc_final: 0.7694 (mp10) REVERT: A 698 PHE cc_start: 0.6181 (m-10) cc_final: 0.5979 (m-10) REVERT: A 702 CYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7462 (p) REVERT: A 722 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 776 PHE cc_start: 0.8827 (m-80) cc_final: 0.8475 (m-80) REVERT: A 779 TYR cc_start: 0.8725 (m-10) cc_final: 0.8230 (m-80) REVERT: B 31 MET cc_start: 0.8712 (mtp) cc_final: 0.8510 (ttp) REVERT: B 405 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: B 574 ARG cc_start: 0.5846 (mmm-85) cc_final: 0.5341 (mmm-85) outliers start: 46 outliers final: 25 residues processed: 170 average time/residue: 0.0950 time to fit residues: 25.3420 Evaluate side-chains 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.103716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070885 restraints weight = 28757.305| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.42 r_work: 0.2990 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12688 Z= 0.165 Angle : 0.614 14.288 17204 Z= 0.296 Chirality : 0.043 0.225 1920 Planarity : 0.004 0.053 2156 Dihedral : 5.577 59.516 1782 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 3.78 % Allowed : 21.14 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 690 sheet: -0.50 (0.42), residues: 159 loop : -1.55 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.028 0.001 TYR B 645 PHE 0.023 0.001 PHE A 776 TRP 0.013 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (12666) covalent geometry : angle 0.60813 / 0.29 (17158) SS BOND : bond 0.00322 / 0.18 ( 20) SS BOND : angle 1.14783 / 0.74 ( 40) hydrogen bonds : bond 0.03845 / 2.59 ( 551) hydrogen bonds : angle 4.15507 / 2.97 ( 1608) link_NAG-ASN : bond 0.00416 / 0.21 ( 2) link_NAG-ASN : angle 3.73839 / 1.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.511 Fit side-chains REVERT: A 277 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8565 (t80) REVERT: A 407 MET cc_start: 0.9023 (tpp) cc_final: 0.8625 (tpt) REVERT: A 442 MET cc_start: 0.9308 (mmt) cc_final: 0.9049 (mmt) REVERT: A 559 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 693 GLN cc_start: 0.8096 (mp10) cc_final: 0.7688 (mp10) REVERT: A 698 PHE cc_start: 0.6221 (m-10) cc_final: 0.6018 (m-10) REVERT: A 702 CYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 722 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8144 (p0) REVERT: A 776 PHE cc_start: 0.8827 (m-80) cc_final: 0.8493 (m-80) REVERT: A 779 TYR cc_start: 0.8752 (m-10) cc_final: 0.8224 (m-80) REVERT: A 817 MET cc_start: 0.8387 (mmm) cc_final: 0.8022 (tpp) REVERT: B 405 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8221 (m-10) REVERT: B 574 ARG cc_start: 0.5878 (mmm-85) cc_final: 0.5368 (mmm-85) REVERT: B 645 TYR cc_start: 0.6945 (p90) cc_final: 0.6594 (p90) REVERT: B 734 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7464 (m110) outliers start: 51 outliers final: 37 residues processed: 176 average time/residue: 0.0947 time to fit residues: 26.2687 Evaluate side-chains 177 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 135 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.103641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070788 restraints weight = 28825.706| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.46 r_work: 0.2990 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12688 Z= 0.165 Angle : 0.614 14.288 17204 Z= 0.296 Chirality : 0.043 0.225 1920 Planarity : 0.004 0.053 2156 Dihedral : 5.577 59.516 1782 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 3.26 % Allowed : 21.36 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1552 helix: 1.19 (0.20), residues: 690 sheet: -0.50 (0.42), residues: 159 loop : -1.55 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.028 0.001 TYR B 645 PHE 0.023 0.001 PHE A 776 TRP 0.013 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (12666) covalent geometry : angle 0.60819 / 0.29 (17158) SS BOND : bond 0.00322 / 0.18 ( 20) SS BOND : angle 1.14781 / 0.74 ( 40) hydrogen bonds : bond 0.03845 / 2.59 ( 551) hydrogen bonds : angle 4.15507 / 2.97 ( 1608) link_NAG-ASN : bond 0.00416 / 0.21 ( 2) link_NAG-ASN : angle 3.73839 / 1.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.490 Fit side-chains REVERT: A 277 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8559 (t80) REVERT: A 407 MET cc_start: 0.9034 (tpp) cc_final: 0.8634 (tpt) REVERT: A 442 MET cc_start: 0.9311 (mmt) cc_final: 0.9052 (mmt) REVERT: A 559 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 693 GLN cc_start: 0.8098 (mp10) cc_final: 0.7690 (mp10) REVERT: A 698 PHE cc_start: 0.6219 (m-10) cc_final: 0.6016 (m-10) REVERT: A 702 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 722 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 776 PHE cc_start: 0.8828 (m-80) cc_final: 0.8495 (m-80) REVERT: A 779 TYR cc_start: 0.8754 (m-10) cc_final: 0.8226 (m-80) REVERT: A 817 MET cc_start: 0.8386 (mmm) cc_final: 0.8022 (tpp) REVERT: B 405 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: B 574 ARG cc_start: 0.5873 (mmm-85) cc_final: 0.5363 (mmm-85) REVERT: B 645 TYR cc_start: 0.6947 (p90) cc_final: 0.6589 (p90) REVERT: B 734 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7457 (m110) outliers start: 44 outliers final: 38 residues processed: 169 average time/residue: 0.0966 time to fit residues: 25.5455 Evaluate side-chains 178 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.103937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071102 restraints weight = 28734.383| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.47 r_work: 0.2978 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12688 Z= 0.133 Angle : 0.600 13.285 17204 Z= 0.292 Chirality : 0.043 0.226 1920 Planarity : 0.003 0.051 2156 Dihedral : 5.502 58.240 1782 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.62 % Rotamer: Outliers : 3.26 % Allowed : 21.66 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.22), residues: 1552 helix: 1.18 (0.20), residues: 690 sheet: -0.52 (0.42), residues: 159 loop : -1.54 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 508 TYR 0.029 0.001 TYR B 645 PHE 0.023 0.001 PHE A 776 TRP 0.011 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (12666) covalent geometry : angle 0.59506 / 0.29 (17158) SS BOND : bond 0.00294 / 0.16 ( 20) SS BOND : angle 1.07489 / 0.69 ( 40) hydrogen bonds : bond 0.03798 / 2.54 ( 551) hydrogen bonds : angle 4.11732 / 2.94 ( 1608) link_NAG-ASN : bond 0.00364 / 0.18 ( 2) link_NAG-ASN : angle 3.45387 / 1.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8530 (t80) REVERT: A 407 MET cc_start: 0.9053 (tpp) cc_final: 0.8656 (tpt) REVERT: A 442 MET cc_start: 0.9319 (mmt) cc_final: 0.9066 (mmt) REVERT: A 559 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 693 GLN cc_start: 0.8169 (mp10) cc_final: 0.7739 (mp10) REVERT: A 702 CYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7449 (p) REVERT: A 722 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8130 (p0) REVERT: A 776 PHE cc_start: 0.8863 (m-80) cc_final: 0.8526 (m-80) REVERT: A 779 TYR cc_start: 0.8772 (m-10) cc_final: 0.8228 (m-80) REVERT: A 817 MET cc_start: 0.8304 (mmm) cc_final: 0.7955 (tpp) REVERT: B 405 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: B 477 ASP cc_start: 0.7192 (t0) cc_final: 0.6967 (t0) REVERT: B 734 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7459 (m110) REVERT: B 768 PHE cc_start: 0.8047 (m-80) cc_final: 0.7474 (m-80) outliers start: 44 outliers final: 35 residues processed: 173 average time/residue: 0.0945 time to fit residues: 25.6450 Evaluate side-chains 177 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 747 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.103941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071145 restraints weight = 28770.060| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.48 r_work: 0.2978 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12688 Z= 0.131 Angle : 0.609 12.786 17204 Z= 0.296 Chirality : 0.043 0.226 1920 Planarity : 0.003 0.050 2156 Dihedral : 5.477 57.231 1782 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.25 % Favored : 93.62 % Rotamer: Outliers : 3.41 % Allowed : 21.66 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1552 helix: 1.14 (0.20), residues: 690 sheet: -0.54 (0.42), residues: 159 loop : -1.53 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 574 TYR 0.030 0.001 TYR B 645 PHE 0.024 0.001 PHE A 756 TRP 0.011 0.001 TRP A 575 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12666) covalent geometry : angle 0.60465 / 0.29 (17158) SS BOND : bond 0.00291 / 0.16 ( 20) SS BOND : angle 1.05142 / 0.68 ( 40) hydrogen bonds : bond 0.03804 / 2.54 ( 551) hydrogen bonds : angle 4.13800 / 2.97 ( 1608) link_NAG-ASN : bond 0.00348 / 0.17 ( 2) link_NAG-ASN : angle 3.32726 / 1.72 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8514 (t80) REVERT: A 407 MET cc_start: 0.9052 (tpp) cc_final: 0.8653 (tpt) REVERT: A 442 MET cc_start: 0.9322 (mmt) cc_final: 0.9070 (mmt) REVERT: A 559 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 693 GLN cc_start: 0.8130 (mp10) cc_final: 0.7713 (mp10) REVERT: A 702 CYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 722 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 776 PHE cc_start: 0.8870 (m-80) cc_final: 0.8541 (m-80) REVERT: A 779 TYR cc_start: 0.8797 (m-10) cc_final: 0.8237 (m-80) REVERT: A 817 MET cc_start: 0.8309 (mmm) cc_final: 0.7981 (tpp) REVERT: B 405 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: B 477 ASP cc_start: 0.7270 (t0) cc_final: 0.7033 (t0) REVERT: B 645 TYR cc_start: 0.6933 (p90) cc_final: 0.6579 (p90) REVERT: B 734 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7413 (m110) REVERT: B 768 PHE cc_start: 0.8044 (m-80) cc_final: 0.7467 (m-80) outliers start: 46 outliers final: 37 residues processed: 170 average time/residue: 0.0883 time to fit residues: 23.5987 Evaluate side-chains 179 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 702 CYS Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 88 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN B 693 GLN B 747 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.101836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.068771 restraints weight = 28949.415| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.47 r_work: 0.2933 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12688 Z= 0.244 Angle : 0.654 11.748 17204 Z= 0.325 Chirality : 0.045 0.257 1920 Planarity : 0.004 0.049 2156 Dihedral : 5.627 55.046 1782 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.17 % Rotamer: Outliers : 3.64 % Allowed : 21.29 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1552 helix: 1.05 (0.20), residues: 700 sheet: -0.66 (0.41), residues: 164 loop : -1.67 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.028 0.002 TYR A 757 PHE 0.020 0.002 PHE A 756 TRP 0.014 0.002 TRP B 785 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (12666) covalent geometry : angle 0.64755 / 0.32 (17158) SS BOND : bond 0.00391 / 0.22 ( 20) SS BOND : angle 1.36135 / 0.87 ( 40) hydrogen bonds : bond 0.04282 / 2.85 ( 551) hydrogen bonds : angle 4.28509 / 3.09 ( 1608) link_NAG-ASN : bond 0.00544 / 0.28 ( 2) link_NAG-ASN : angle 3.85482 / 2.03 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.71 seconds wall clock time: 69 minutes 0.02 seconds (4140.02 seconds total)