Starting phenix.real_space_refine on Sun May 3 08:49:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0c_37974/05_2026/8x0c_37974.cif" } resolution = 3.2 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= 0.001 sd= 0.064 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 116 5.16 5 C 7832 2.51 5 N 2016 2.21 5 O 2214 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 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 6039 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 32, 'TRANS': 735} Chain breaks: 2 Chain: "B" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 6039 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 32, 'TRANS': 735} Chain breaks: 2 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 Time building chain proxies: 3.05, per 1000 atoms: 0.25 Number of scatterers: 12180 At special positions: 0 Unit cell: (81.8072, 95.1009, 177.931, 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 116 16.00 F 2 9.00 O 2214 8.00 N 2016 7.00 C 7832 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=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.03 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=2.03 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=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 576.1 milliseconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 15 sheets defined 49.1% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.606A pdb=" N GLU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.631A 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: 3.510A pdb=" N LEU A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.541A 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: 3.730A 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: 3.541A pdb=" N ALA A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.549A 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: 3.831A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.822A pdb=" N LYS A 430 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.544A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.709A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 675 removed outlier: 3.637A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.890A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 715 removed outlier: 3.616A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 762 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 769 through 788 removed outlier: 3.608A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 797 through 817 Processing helix chain 'A' and resid 818 through 827 removed outlier: 3.852A pdb=" N ALA A 827 " --> pdb=" O TYR A 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.649A pdb=" N GLU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.650A 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: 3.558A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 209 removed outlier: 4.109A pdb=" N GLN B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.857A 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 310 through 314 removed outlier: 3.769A pdb=" N VAL B 313 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 314' Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.557A pdb=" N ALA B 321 " --> pdb=" O TYR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.572A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 removed outlier: 3.661A 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 Processing helix chain 'B' and resid 616 through 636 removed outlier: 5.733A pdb=" N LEU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 675 removed outlier: 3.685A pdb=" N TYR B 645 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 4.568A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 673 " --> pdb=" O ILE B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 removed outlier: 3.721A pdb=" N ILE B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 762 removed outlier: 3.895A 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: 4.358A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 788 " --> pdb=" O ILE B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 818 through 827 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.203A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN A 169 " --> pdb=" O MET A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248 removed outlier: 8.212A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N TYR A 213 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ALA A 275 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.693A 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: 6.660A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.387A 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 524 Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.813A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 719 through 720 removed outlier: 3.618A pdb=" N MET A 720 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 732 " --> pdb=" O MET A 720 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.372A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 241 through 248 removed outlier: 7.927A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 213 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALA B 275 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE B 277 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 217 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.761A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 523 Processing sheet with id=AB4, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AB5, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AB6, first strand: chain 'B' and resid 719 through 722 574 hydrogen bonds defined for protein. 1692 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: 2.20 Time building geometry restraints manager: 1.31 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: 2157 1.32 - 1.45: 3477 1.45 - 1.58: 6656 1.58 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 12458 Sorted by residual: bond pdb=" CA SER A 654 " pdb=" CB SER A 654 " ideal model delta sigma weight residual 1.534 1.508 0.027 1.18e-02 7.18e+03 5.06e+00 bond pdb=" CA SER B 462 " pdb=" CB SER B 462 " ideal model delta sigma weight residual 1.537 1.507 0.031 1.38e-02 5.25e+03 4.92e+00 bond pdb=" CA LEU B 86 " pdb=" CB LEU B 86 " ideal model delta sigma weight residual 1.522 1.537 -0.015 7.00e-03 2.04e+04 4.60e+00 bond pdb=" CA SER A 462 " pdb=" CB SER A 462 " ideal model delta sigma weight residual 1.536 1.506 0.030 1.46e-02 4.69e+03 4.26e+00 bond pdb=" CA SER A 304 " pdb=" CB SER A 304 " ideal model delta sigma weight residual 1.535 1.508 0.026 1.32e-02 5.74e+03 4.01e+00 ... (remaining 12453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16548 2.09 - 4.19: 315 4.19 - 6.28: 14 6.28 - 8.37: 4 8.37 - 10.46: 3 Bond angle restraints: 16884 Sorted by residual: angle pdb=" C03 QUS A 902 " pdb=" N14 QUS A 902 " pdb=" O20 QUS A 902 " ideal model delta sigma weight residual 112.77 123.23 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CA ASP B 722 " pdb=" CB ASP B 722 " pdb=" CG ASP B 722 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C03 QUS B 902 " pdb=" N14 QUS B 902 " pdb=" O20 QUS B 902 " ideal model delta sigma weight residual 112.77 122.67 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N TYR B 619 " pdb=" CA TYR B 619 " pdb=" C TYR B 619 " ideal model delta sigma weight residual 113.18 109.00 4.18 1.33e+00 5.65e-01 9.90e+00 ... (remaining 16879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 7231 33.37 - 66.73: 255 66.73 - 100.10: 21 100.10 - 133.47: 7 133.47 - 166.84: 2 Dihedral angle restraints: 7516 sinusoidal: 3048 harmonic: 4468 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual -86.00 -173.96 87.96 1 1.00e+01 1.00e-02 9.26e+01 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 -9.67 -76.33 1 1.00e+01 1.00e-02 7.33e+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 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 ... (remaining 7513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1629 0.093 - 0.186: 258 0.186 - 0.280: 3 0.280 - 0.373: 1 0.373 - 0.466: 1 Chirality restraints: 1892 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 5.43e+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 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+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 2.45 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1889 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 XQT B 903 " -0.069 2.00e-02 2.50e+03 5.71e-02 4.07e+01 pdb=" C6 XQT B 903 " 0.022 2.00e-02 2.50e+03 pdb=" C7 XQT B 903 " -0.053 2.00e-02 2.50e+03 pdb=" N1 XQT B 903 " 0.090 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 XQT A 903 " -0.037 2.00e-02 2.50e+03 3.15e-02 1.24e+01 pdb=" C6 XQT A 903 " 0.020 2.00e-02 2.50e+03 pdb=" C7 XQT A 903 " -0.031 2.00e-02 2.50e+03 pdb=" N1 XQT A 903 " 0.046 2.00e-02 2.50e+03 pdb=" O2 XQT A 903 " 0.003 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 2.02e-02 9.20e+00 pdb=" C12 XQT B 903 " -0.030 2.00e-02 2.50e+03 pdb=" C13 XQT B 903 " -0.024 2.00e-02 2.50e+03 pdb=" C14 XQT B 903 " -0.011 2.00e-02 2.50e+03 pdb=" C15 XQT B 903 " 0.002 2.00e-02 2.50e+03 pdb=" C16 XQT B 903 " 0.011 2.00e-02 2.50e+03 pdb=" C17 XQT B 903 " 0.012 2.00e-02 2.50e+03 pdb=" C18 XQT B 903 " -0.008 2.00e-02 2.50e+03 pdb=" F1 XQT B 903 " 0.007 2.00e-02 2.50e+03 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 935 2.75 - 3.28: 12896 3.28 - 3.82: 20595 3.82 - 4.36: 24527 4.36 - 4.90: 41554 Nonbonded interactions: 100507 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" O SER B 395 " model vdw 2.208 3.040 nonbonded pdb=" OG SER A 654 " pdb=" F1 XQT A 903 " model vdw 2.215 2.990 nonbonded pdb=" NH2 ARG A 648 " pdb=" O ASN A 734 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.230 3.040 ... (remaining 100502 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: 1.050 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.820 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12480 Z= 0.416 Angle : 0.821 10.464 16930 Z= 0.520 Chirality : 0.062 0.466 1892 Planarity : 0.005 0.057 2124 Dihedral : 16.845 166.836 4592 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 0.53 % Allowed : 17.60 % Favored : 81.87 % 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: -0.59 (0.21), residues: 1524 helix: 0.76 (0.20), residues: 697 sheet: -0.70 (0.40), residues: 157 loop : -1.56 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 292 TYR 0.019 0.003 TYR B 572 PHE 0.016 0.003 PHE B 165 TRP 0.022 0.003 TRP A 575 HIS 0.009 0.002 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00647 (12458) covalent geometry : angle 0.81819 (16884) SS BOND : bond 0.00716 ( 20) SS BOND : angle 1.35074 ( 40) hydrogen bonds : bond 0.14416 ( 574) hydrogen bonds : angle 5.71208 ( 1692) link_NAG-ASN : bond 0.00580 ( 2) link_NAG-ASN : angle 2.36749 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.7954 (mmtm) REVERT: B 491 GLU cc_start: 0.7543 (tp30) cc_final: 0.7273 (tp30) outliers start: 7 outliers final: 3 residues processed: 159 average time/residue: 0.0936 time to fit residues: 23.0730 Evaluate side-chains 152 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 572 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129984 restraints weight = 15727.025| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.62 r_work: 0.3036 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12480 Z= 0.197 Angle : 0.632 8.728 16930 Z= 0.318 Chirality : 0.045 0.213 1892 Planarity : 0.004 0.051 2124 Dihedral : 9.523 98.500 1765 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 2.27 % Allowed : 16.99 % Favored : 80.74 % 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: -0.36 (0.22), residues: 1524 helix: 1.09 (0.20), residues: 710 sheet: -1.00 (0.39), residues: 169 loop : -1.54 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 648 TYR 0.019 0.001 TYR B 645 PHE 0.018 0.001 PHE B 337 TRP 0.010 0.001 TRP B 336 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00460 (12458) covalent geometry : angle 0.62998 (16884) SS BOND : bond 0.00428 ( 20) SS BOND : angle 1.09865 ( 40) hydrogen bonds : bond 0.05264 ( 574) hydrogen bonds : angle 4.55466 ( 1692) link_NAG-ASN : bond 0.00191 ( 2) link_NAG-ASN : angle 1.64169 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6777 (p0) cc_final: 0.6229 (t0) REVERT: B 277 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.7560 (t80) outliers start: 30 outliers final: 17 residues processed: 176 average time/residue: 0.0985 time to fit residues: 26.6835 Evaluate side-chains 169 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 733 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.172669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132849 restraints weight = 15919.200| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.18 r_work: 0.3093 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12480 Z= 0.154 Angle : 0.602 9.717 16930 Z= 0.299 Chirality : 0.044 0.205 1892 Planarity : 0.004 0.053 2124 Dihedral : 8.141 91.257 1754 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 3.70 % Allowed : 16.92 % Favored : 79.38 % 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: -0.24 (0.21), residues: 1524 helix: 1.19 (0.20), residues: 713 sheet: -0.84 (0.40), residues: 164 loop : -1.54 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 648 TYR 0.021 0.001 TYR A 209 PHE 0.014 0.001 PHE B 544 TRP 0.018 0.001 TRP B 532 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00349 (12458) covalent geometry : angle 0.59992 (16884) SS BOND : bond 0.00385 ( 20) SS BOND : angle 1.03301 ( 40) hydrogen bonds : bond 0.04694 ( 574) hydrogen bonds : angle 4.39361 ( 1692) link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 1.81532 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 ASN cc_start: 0.7063 (p0) cc_final: 0.6785 (p0) REVERT: A 796 ASN cc_start: 0.6344 (p0) cc_final: 0.5904 (t0) REVERT: B 277 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7602 (t80) REVERT: B 406 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8785 (m) outliers start: 49 outliers final: 27 residues processed: 194 average time/residue: 0.0952 time to fit residues: 28.5356 Evaluate side-chains 181 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 733 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129780 restraints weight = 15669.378| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.14 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12480 Z= 0.176 Angle : 0.617 11.163 16930 Z= 0.304 Chirality : 0.044 0.202 1892 Planarity : 0.004 0.051 2124 Dihedral : 7.065 79.641 1754 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 4.15 % Allowed : 17.15 % Favored : 78.70 % 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: -0.20 (0.21), residues: 1524 helix: 1.23 (0.19), residues: 714 sheet: -0.91 (0.39), residues: 163 loop : -1.50 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 524 TYR 0.019 0.001 TYR A 209 PHE 0.015 0.001 PHE B 544 TRP 0.015 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00406 (12458) covalent geometry : angle 0.61430 (16884) SS BOND : bond 0.00373 ( 20) SS BOND : angle 1.02982 ( 40) hydrogen bonds : bond 0.04573 ( 574) hydrogen bonds : angle 4.32107 ( 1692) link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 2.47346 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6265 (p0) cc_final: 0.5843 (t0) REVERT: B 72 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8330 (ttt) REVERT: B 277 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7535 (t80) REVERT: B 429 MET cc_start: 0.7348 (mmm) cc_final: 0.7029 (mmm) REVERT: B 804 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6997 (m-10) outliers start: 55 outliers final: 36 residues processed: 200 average time/residue: 0.0932 time to fit residues: 28.8579 Evaluate side-chains 198 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 776 PHE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 overall best weight: 1.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.171867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133113 restraints weight = 15808.598| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.89 r_work: 0.3082 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12480 Z= 0.159 Angle : 0.611 11.596 16930 Z= 0.299 Chirality : 0.043 0.208 1892 Planarity : 0.004 0.051 2124 Dihedral : 6.424 62.970 1754 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 4.08 % Allowed : 18.05 % Favored : 77.87 % 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: -0.23 (0.21), residues: 1524 helix: 1.19 (0.19), residues: 728 sheet: -0.89 (0.40), residues: 163 loop : -1.55 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 727 TYR 0.016 0.001 TYR A 209 PHE 0.014 0.001 PHE A 337 TRP 0.014 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00367 (12458) covalent geometry : angle 0.60698 (16884) SS BOND : bond 0.00374 ( 20) SS BOND : angle 1.11028 ( 40) hydrogen bonds : bond 0.04385 ( 574) hydrogen bonds : angle 4.25803 ( 1692) link_NAG-ASN : bond 0.00350 ( 2) link_NAG-ASN : angle 3.04308 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6163 (p0) cc_final: 0.5815 (t0) REVERT: B 72 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8196 (ttt) REVERT: B 85 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8213 (tt) REVERT: B 277 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.7666 (t80) REVERT: B 406 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8802 (m) REVERT: B 429 MET cc_start: 0.7319 (mmm) cc_final: 0.7085 (mmm) REVERT: B 508 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.4998 (mtm-85) REVERT: B 804 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.6960 (m-10) outliers start: 54 outliers final: 37 residues processed: 201 average time/residue: 0.0947 time to fit residues: 29.3499 Evaluate side-chains 199 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 139 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.169692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.129367 restraints weight = 15721.438| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.59 r_work: 0.3056 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12480 Z= 0.240 Angle : 0.654 11.412 16930 Z= 0.325 Chirality : 0.045 0.219 1892 Planarity : 0.004 0.049 2124 Dihedral : 6.206 59.079 1754 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 4.46 % Allowed : 18.20 % Favored : 77.34 % 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: -0.33 (0.21), residues: 1524 helix: 1.09 (0.19), residues: 732 sheet: -0.96 (0.38), residues: 168 loop : -1.60 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 524 TYR 0.018 0.002 TYR A 209 PHE 0.018 0.002 PHE B 337 TRP 0.012 0.002 TRP B 532 HIS 0.006 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00567 (12458) covalent geometry : angle 0.64725 (16884) SS BOND : bond 0.00452 ( 20) SS BOND : angle 1.22827 ( 40) hydrogen bonds : bond 0.04783 ( 574) hydrogen bonds : angle 4.33418 ( 1692) link_NAG-ASN : bond 0.00552 ( 2) link_NAG-ASN : angle 4.23464 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8180 (mttt) cc_final: 0.7969 (mppt) REVERT: A 508 ARG cc_start: 0.7162 (ptt-90) cc_final: 0.6817 (mpp-170) REVERT: A 796 ASN cc_start: 0.6346 (p0) cc_final: 0.5950 (t0) REVERT: B 72 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7996 (ttt) REVERT: B 85 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 277 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.7909 (t80) REVERT: B 406 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8800 (m) REVERT: B 429 MET cc_start: 0.7211 (mmm) cc_final: 0.6978 (mmm) REVERT: B 497 ASP cc_start: 0.7229 (m-30) cc_final: 0.6669 (t70) REVERT: B 508 ARG cc_start: 0.6458 (OUTLIER) cc_final: 0.5056 (mtm-85) REVERT: B 804 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6807 (m-10) REVERT: B 814 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7683 (tt) REVERT: B 817 MET cc_start: 0.6792 (ttt) cc_final: 0.6133 (tmm) outliers start: 59 outliers final: 41 residues processed: 206 average time/residue: 0.0987 time to fit residues: 30.6302 Evaluate side-chains 206 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129671 restraints weight = 15659.474| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.47 r_work: 0.3108 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 0.029 12480 Z= 0.124 Angle : 0.598 10.475 16930 Z= 0.294 Chirality : 0.042 0.218 1892 Planarity : 0.004 0.049 2124 Dihedral : 5.853 59.304 1754 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 3.40 % Allowed : 19.71 % Favored : 76.89 % 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: -0.15 (0.21), residues: 1524 helix: 1.29 (0.19), residues: 714 sheet: -0.75 (0.40), residues: 158 loop : -1.55 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 648 TYR 0.018 0.001 TYR A 209 PHE 0.015 0.001 PHE A 712 TRP 0.013 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00275 (12458) covalent geometry : angle 0.59335 (16884) SS BOND : bond 0.00339 ( 20) SS BOND : angle 0.96630 ( 40) hydrogen bonds : bond 0.04193 ( 574) hydrogen bonds : angle 4.21946 ( 1692) link_NAG-ASN : bond 0.00519 ( 2) link_NAG-ASN : angle 3.42859 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6257 (p0) cc_final: 0.5883 (t0) REVERT: B 72 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: B 277 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7758 (t80) REVERT: B 281 MET cc_start: 0.8693 (mmp) cc_final: 0.8355 (mmp) REVERT: B 406 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8793 (m) REVERT: B 429 MET cc_start: 0.7364 (mmm) cc_final: 0.7160 (mmm) REVERT: B 508 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5018 (mtm-85) REVERT: B 636 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7742 (pt) REVERT: B 804 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: B 814 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7650 (tt) REVERT: B 817 MET cc_start: 0.6723 (ttt) cc_final: 0.6127 (tmm) outliers start: 45 outliers final: 27 residues processed: 195 average time/residue: 0.0938 time to fit residues: 27.9098 Evaluate side-chains 188 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.171107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131915 restraints weight = 15680.824| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.73 r_work: 0.3111 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12480 Z= 0.171 Angle : 0.629 15.495 16930 Z= 0.307 Chirality : 0.043 0.217 1892 Planarity : 0.004 0.049 2124 Dihedral : 5.753 59.762 1754 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 3.93 % Allowed : 19.71 % Favored : 76.36 % 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: -0.18 (0.21), residues: 1524 helix: 1.27 (0.19), residues: 715 sheet: -0.96 (0.39), residues: 168 loop : -1.51 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 727 TYR 0.034 0.001 TYR B 746 PHE 0.013 0.001 PHE B 337 TRP 0.013 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00400 (12458) covalent geometry : angle 0.62575 (16884) SS BOND : bond 0.00379 ( 20) SS BOND : angle 1.04483 ( 40) hydrogen bonds : bond 0.04317 ( 574) hydrogen bonds : angle 4.23835 ( 1692) link_NAG-ASN : bond 0.00422 ( 2) link_NAG-ASN : angle 2.94639 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6391 (p0) cc_final: 0.5967 (t0) REVERT: B 72 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8303 (ttt) REVERT: B 277 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.7783 (t80) REVERT: B 406 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8846 (m) REVERT: B 429 MET cc_start: 0.7382 (mmm) cc_final: 0.7163 (mmm) REVERT: B 497 ASP cc_start: 0.7330 (m-30) cc_final: 0.6663 (t70) REVERT: B 508 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5239 (mtm-85) REVERT: B 636 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7747 (pt) REVERT: B 804 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6971 (m-10) REVERT: B 814 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7710 (tt) REVERT: B 817 MET cc_start: 0.6754 (ttt) cc_final: 0.6112 (tmm) outliers start: 52 outliers final: 39 residues processed: 190 average time/residue: 0.0945 time to fit residues: 27.4817 Evaluate side-chains 200 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 643 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Chi-restraints excluded: chain B residue 814 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 0.0000 chunk 86 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.129962 restraints weight = 15730.183| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.68 r_work: 0.3087 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12480 Z= 0.149 Angle : 0.623 13.925 16930 Z= 0.305 Chirality : 0.043 0.218 1892 Planarity : 0.004 0.049 2124 Dihedral : 5.707 59.731 1754 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 3.55 % Allowed : 19.94 % Favored : 76.51 % 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: -0.16 (0.21), residues: 1524 helix: 1.28 (0.19), residues: 718 sheet: -0.95 (0.39), residues: 168 loop : -1.49 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 524 TYR 0.015 0.001 TYR B 645 PHE 0.012 0.001 PHE B 337 TRP 0.013 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00342 (12458) covalent geometry : angle 0.62051 (16884) SS BOND : bond 0.00362 ( 20) SS BOND : angle 0.98960 ( 40) hydrogen bonds : bond 0.04223 ( 574) hydrogen bonds : angle 4.22899 ( 1692) link_NAG-ASN : bond 0.00337 ( 2) link_NAG-ASN : angle 2.52316 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 796 ASN cc_start: 0.6287 (p0) cc_final: 0.5911 (t0) REVERT: B 72 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8160 (ttt) REVERT: B 277 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 406 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8782 (m) REVERT: B 508 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5110 (mtm-85) REVERT: B 636 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7699 (pt) REVERT: B 804 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: B 817 MET cc_start: 0.6762 (ttt) cc_final: 0.6221 (tmm) outliers start: 47 outliers final: 32 residues processed: 187 average time/residue: 0.0938 time to fit residues: 26.4745 Evaluate side-chains 188 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130059 restraints weight = 15776.896| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.70 r_work: 0.3121 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12480 Z= 0.128 Angle : 0.626 13.604 16930 Z= 0.304 Chirality : 0.043 0.218 1892 Planarity : 0.004 0.049 2124 Dihedral : 5.662 59.535 1754 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.14 % Rotamer: Outliers : 3.32 % Allowed : 19.94 % Favored : 76.74 % 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: -0.12 (0.21), residues: 1524 helix: 1.29 (0.19), residues: 716 sheet: -0.79 (0.40), residues: 158 loop : -1.48 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 524 TYR 0.016 0.001 TYR A 209 PHE 0.014 0.001 PHE A 337 TRP 0.014 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00288 (12458) covalent geometry : angle 0.62381 (16884) SS BOND : bond 0.00351 ( 20) SS BOND : angle 0.97496 ( 40) hydrogen bonds : bond 0.04083 ( 574) hydrogen bonds : angle 4.18818 ( 1692) link_NAG-ASN : bond 0.00334 ( 2) link_NAG-ASN : angle 2.27252 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 439 GLU cc_start: 0.8503 (tp30) cc_final: 0.8263 (tp30) REVERT: A 734 ASN cc_start: 0.7301 (p0) cc_final: 0.7033 (p0) REVERT: A 796 ASN cc_start: 0.6347 (p0) cc_final: 0.5941 (t0) REVERT: B 72 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8388 (ttt) REVERT: B 277 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 406 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8874 (m) REVERT: B 497 ASP cc_start: 0.7315 (m-30) cc_final: 0.6623 (t70) REVERT: B 508 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5270 (mtm-85) REVERT: B 636 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7686 (pt) REVERT: B 804 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7007 (m-10) REVERT: B 817 MET cc_start: 0.6805 (ttt) cc_final: 0.6240 (tmm) outliers start: 44 outliers final: 33 residues processed: 181 average time/residue: 0.0928 time to fit residues: 25.5042 Evaluate side-chains 191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 SER 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 313 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 733 CYS Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 7.9990 chunk 149 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 121 optimal weight: 0.0020 chunk 24 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.172167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129903 restraints weight = 15753.448| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.20 r_work: 0.3122 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12480 Z= 0.128 Angle : 0.626 13.597 16930 Z= 0.303 Chirality : 0.043 0.218 1892 Planarity : 0.004 0.049 2124 Dihedral : 5.671 59.535 1754 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.14 % Rotamer: Outliers : 3.10 % Allowed : 19.86 % Favored : 77.04 % 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: -0.12 (0.21), residues: 1524 helix: 1.29 (0.19), residues: 716 sheet: -0.79 (0.40), residues: 158 loop : -1.48 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 727 TYR 0.016 0.001 TYR A 209 PHE 0.014 0.001 PHE A 337 TRP 0.014 0.001 TRP B 532 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00288 (12458) covalent geometry : angle 0.62358 (16884) SS BOND : bond 0.00350 ( 20) SS BOND : angle 0.97491 ( 40) hydrogen bonds : bond 0.04083 ( 574) hydrogen bonds : angle 4.18816 ( 1692) link_NAG-ASN : bond 0.00334 ( 2) link_NAG-ASN : angle 2.27252 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3027.65 seconds wall clock time: 52 minutes 37.35 seconds (3157.35 seconds total)