Starting phenix.real_space_refine on Fri Jul 3 11:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.map" model { file = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aio_11800/07_2026/7aio_11800.cif" } resolution = 3.31 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 94 5.16 5 C 9028 2.51 5 N 2308 2.21 5 O 2485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13915 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 6918 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 34, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "A" Number of atoms: 6891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 6891 Classifications: {'peptide': 909} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 34, 'TRANS': 874} Chain breaks: 3 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 2, 'GLN:plan1': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.03, per 1000 atoms: 0.22 Number of scatterers: 13915 At special positions: 0 Unit cell: (104.811, 93.093, 147.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 94 16.00 O 2485 8.00 N 2308 7.00 C 9028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.02 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN B 328 " " NAG G 1 " - " ASN A 328 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 561.9 milliseconds 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3354 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.659A pdb=" N THR B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 135 through 149 removed outlier: 5.137A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.320A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.559A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.685A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 370 through 376 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.521A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.742A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.704A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.229A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.943A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.760A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.679A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.663A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.616A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.216A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.538A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.547A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 899 through 917 removed outlier: 4.067A pdb=" N GLN B 904 " --> pdb=" O ASP B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.931A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1066 through 1078 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.710A pdb=" N THR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.246A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.327A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.570A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 256 through 284 removed outlier: 3.606A pdb=" N MET A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.724A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.523A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.704A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.662A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.253A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.925A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.648A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.625A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.679A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.566A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.598A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.244A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.886A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.585A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.652A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 902 through 917 Processing helix chain 'A' and resid 932 through 949 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.928A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.594A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.633A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 858 through 860 removed outlier: 9.716A pdb=" N GLU B 921 " --> pdb=" O CYS B 888 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.554A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.646A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.860A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2382 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: 1.77 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3310 1.33 - 1.45: 2891 1.45 - 1.57: 7877 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14228 Sorted by residual: bond pdb=" N ILE A 250 " pdb=" CA ILE A 250 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.20e+00 bond pdb=" N ILE B 250 " pdb=" CA ILE B 250 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N GLU B1093 " pdb=" CA GLU B1093 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.22e-02 6.72e+03 6.93e+00 bond pdb=" N GLN B 897 " pdb=" CA GLN B 897 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" N ARG B 334 " pdb=" CA ARG B 334 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.69e+00 ... (remaining 14223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 18954 2.38 - 4.76: 371 4.76 - 7.14: 25 7.14 - 9.52: 5 9.52 - 11.89: 1 Bond angle restraints: 19356 Sorted by residual: angle pdb=" C ILE B 639 " pdb=" N CYS B 640 " pdb=" CA CYS B 640 " ideal model delta sigma weight residual 122.38 113.67 8.71 1.81e+00 3.05e-01 2.32e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 111.60 5.03 1.16e+00 7.43e-01 1.88e+01 angle pdb=" N ASN B 266 " pdb=" CA ASN B 266 " pdb=" C ASN B 266 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 116.43 6.10 1.61e+00 3.86e-01 1.44e+01 angle pdb=" CA ILE A 250 " pdb=" C ILE A 250 " pdb=" O ILE A 250 " ideal model delta sigma weight residual 120.95 117.02 3.93 1.04e+00 9.25e-01 1.43e+01 ... (remaining 19351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 7678 17.22 - 34.44: 498 34.44 - 51.66: 78 51.66 - 68.88: 30 68.88 - 86.10: 3 Dihedral angle restraints: 8287 sinusoidal: 3071 harmonic: 5216 Sorted by residual: dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" C ASN B 265 " pdb=" N ASN B 265 " pdb=" CA ASN B 265 " pdb=" CB ASN B 265 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 8284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.960: 2294 0.960 - 1.920: 0 1.920 - 2.880: 0 2.880 - 3.840: 0 3.840 - 4.800: 1 Chirality restraints: 2295 Sorted by residual: chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 2.40 -4.80 2.00e-01 2.50e+01 5.76e+02 chirality pdb=" CA CYS A 640 " pdb=" N CYS A 640 " pdb=" C CYS A 640 " pdb=" CB CYS A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ASN B 265 " pdb=" N ASN B 265 " pdb=" C ASN B 265 " pdb=" CB ASN B 265 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2292 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1101 " 0.202 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" C7 NAG B1101 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG B1101 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG B1101 " -0.282 2.00e-02 2.50e+03 pdb=" O7 NAG B1101 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.090 9.50e-02 1.11e+02 5.47e-02 1.79e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.098 9.50e-02 1.11e+02 5.64e-02 1.70e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.019 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1710 2.74 - 3.28: 14723 3.28 - 3.82: 23398 3.82 - 4.36: 27386 4.36 - 4.90: 47358 Nonbonded interactions: 114575 Sorted by model distance: nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.205 3.120 nonbonded pdb=" O PRO A1058 " pdb=" OH TYR A1070 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN A 376 " pdb=" N SER A 415 " model vdw 2.285 3.120 nonbonded pdb=" NH1 ARG B 680 " pdb=" O PRO A 698 " model vdw 2.286 3.120 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.286 3.120 ... (remaining 114570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 947 or resid 1029 through 1101)) selection = (chain 'B' and (resid 102 through 896 or (resid 901 and (name N or name CA or na \ me C or name O or name CB )) or resid 902 through 907 or (resid 908 through 915 \ and (name N or name CA or name C or name O or name CB )) or resid 916 through 94 \ 6 or (resid 1028 and (name N or name CA or name C or name O or name CB )) or res \ id 1029 through 1101)) } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 0.054 14242 Z= 0.288 Angle : 0.808 11.895 19392 Z= 0.472 Chirality : 0.112 4.800 2295 Planarity : 0.007 0.172 2410 Dihedral : 12.196 86.100 4915 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.01 % Rotamer: Outliers : 0.83 % Allowed : 5.76 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 1805 helix: -0.33 (0.15), residues: 1001 sheet: -1.74 (0.43), residues: 102 loop : -1.84 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.002 ARG B 497 TYR 0.017 0.002 TYR A 937 PHE 0.018 0.002 PHE A 877 TRP 0.036 0.002 TRP A 649 HIS 0.009 0.001 HIS B 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.29 (14228) covalent geometry : angle 0.78984 / 0.47 (19356) SS BOND : bond 0.00467 / 0.23 ( 6) SS BOND : angle 2.30562 / 1.35 ( 12) hydrogen bonds : bond 0.11399 / 7.71 ( 824) hydrogen bonds : angle 5.37143 / 3.85 ( 2382) link_BETA1-4 : bond 0.00178 / 0.09 ( 4) link_BETA1-4 : angle 4.28027 / 2.22 ( 12) link_NAG-ASN : bond 0.00509 / 0.25 ( 4) link_NAG-ASN : angle 5.01432 / 2.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 313 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4020 (tpt) cc_final: 0.3652 (tpt) outliers start: 12 outliers final: 1 residues processed: 322 average time/residue: 0.1205 time to fit residues: 55.9466 Evaluate side-chains 175 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1093 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 382 GLN ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN B 752 ASN B 882 HIS B1069 ASN A 133 GLN A 629 HIS A 752 ASN A 882 HIS A1045 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.132126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.100791 restraints weight = 25621.181| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.45 r_work: 0.3389 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14242 Z= 0.153 Angle : 0.707 22.944 19392 Z= 0.345 Chirality : 0.048 0.921 2295 Planarity : 0.004 0.044 2410 Dihedral : 4.493 54.843 1931 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 1.53 % Allowed : 13.59 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1805 helix: 0.80 (0.16), residues: 1010 sheet: -1.61 (0.43), residues: 112 loop : -1.41 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 785 TYR 0.021 0.001 TYR B 937 PHE 0.019 0.002 PHE B 634 TRP 0.017 0.001 TRP A 649 HIS 0.004 0.001 HIS A 790 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14228) covalent geometry : angle 0.66669 / 0.34 (19356) SS BOND : bond 0.00270 / 0.13 ( 6) SS BOND : angle 1.75388 / 1.04 ( 12) hydrogen bonds : bond 0.04545 / 3.09 ( 824) hydrogen bonds : angle 4.57508 / 3.27 ( 2382) link_BETA1-4 : bond 0.00822 / 0.42 ( 4) link_BETA1-4 : angle 3.34428 / 1.68 ( 12) link_NAG-ASN : bond 0.01108 / 0.53 ( 4) link_NAG-ASN : angle 8.73048 / 4.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4348 (tpt) cc_final: 0.3753 (tpt) REVERT: B 107 ASN cc_start: 0.7514 (p0) cc_final: 0.7285 (p0) REVERT: B 381 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6232 (mt) REVERT: B 601 MET cc_start: 0.8893 (tpp) cc_final: 0.8689 (tpp) REVERT: B 661 MET cc_start: 0.7375 (tmm) cc_final: 0.7090 (ttm) REVERT: B 673 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8445 (mtmm) REVERT: B 703 ASN cc_start: 0.7424 (m-40) cc_final: 0.7091 (t0) REVERT: B 760 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: B 1040 ASN cc_start: 0.8885 (m-40) cc_final: 0.8220 (m110) REVERT: B 1046 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8987 (mmtm) REVERT: A 329 ARG cc_start: 0.7581 (mmt90) cc_final: 0.7196 (mmt90) REVERT: A 353 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8349 (mtmm) REVERT: A 580 GLU cc_start: 0.8021 (tp30) cc_final: 0.7671 (tp30) outliers start: 22 outliers final: 11 residues processed: 231 average time/residue: 0.0912 time to fit residues: 32.6818 Evaluate side-chains 185 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 760 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 629 HIS B1069 ASN A 120 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.125419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.094117 restraints weight = 26274.436| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.43 r_work: 0.3307 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14242 Z= 0.243 Angle : 0.719 21.970 19392 Z= 0.353 Chirality : 0.047 0.567 2295 Planarity : 0.004 0.039 2410 Dihedral : 4.241 22.195 1928 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 2.91 % Allowed : 14.01 % Favored : 83.08 % 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: -0.03 (0.19), residues: 1805 helix: 0.96 (0.16), residues: 1007 sheet: -1.49 (0.44), residues: 112 loop : -1.19 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 939 TYR 0.017 0.002 TYR B 937 PHE 0.016 0.002 PHE A 555 TRP 0.012 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (14228) covalent geometry : angle 0.68421 / 0.34 (19356) SS BOND : bond 0.00620 / 0.32 ( 6) SS BOND : angle 1.78942 / 1.04 ( 12) hydrogen bonds : bond 0.04465 / 3.05 ( 824) hydrogen bonds : angle 4.52809 / 3.24 ( 2382) link_BETA1-4 : bond 0.00184 / 0.09 ( 4) link_BETA1-4 : angle 3.20932 / 1.63 ( 12) link_NAG-ASN : bond 0.01126 / 0.54 ( 4) link_NAG-ASN : angle 8.10965 / 4.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4596 (tpt) cc_final: 0.3929 (tpt) REVERT: B 138 MET cc_start: 0.8355 (tpp) cc_final: 0.8007 (tpp) REVERT: B 278 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7631 (mtp) REVERT: B 381 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6547 (mt) REVERT: B 673 LYS cc_start: 0.8807 (mtmm) cc_final: 0.8507 (mtmm) REVERT: A 329 ARG cc_start: 0.7750 (mmt90) cc_final: 0.7512 (mpt-90) REVERT: A 353 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8430 (mtmm) outliers start: 42 outliers final: 24 residues processed: 204 average time/residue: 0.1039 time to fit residues: 32.1367 Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 640 CYS Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 30.0000 chunk 176 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 143 optimal weight: 0.0470 chunk 175 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 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 = 0.3962 r_free = 0.3962 target = 0.130650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099941 restraints weight = 25839.724| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.43 r_work: 0.3390 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14242 Z= 0.126 Angle : 0.629 20.975 19392 Z= 0.306 Chirality : 0.044 0.483 2295 Planarity : 0.004 0.034 2410 Dihedral : 4.079 22.580 1928 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 2.70 % Allowed : 15.19 % Favored : 82.11 % 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: 0.39 (0.20), residues: 1805 helix: 1.34 (0.16), residues: 1008 sheet: -1.32 (0.45), residues: 121 loop : -1.07 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1062 TYR 0.014 0.001 TYR B 937 PHE 0.020 0.001 PHE A 442 TRP 0.013 0.001 TRP B 649 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14228) covalent geometry : angle 0.59483 / 0.30 (19356) SS BOND : bond 0.00580 / 0.27 ( 6) SS BOND : angle 1.64071 / 0.96 ( 12) hydrogen bonds : bond 0.04006 / 2.73 ( 824) hydrogen bonds : angle 4.30269 / 3.09 ( 2382) link_BETA1-4 : bond 0.00598 / 0.30 ( 4) link_BETA1-4 : angle 2.97862 / 1.52 ( 12) link_NAG-ASN : bond 0.01201 / 0.57 ( 4) link_NAG-ASN : angle 7.58405 / 4.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4652 (tpt) cc_final: 0.3977 (tpt) REVERT: B 116 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7771 (pt0) REVERT: B 381 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6523 (mt) REVERT: B 601 MET cc_start: 0.8753 (tpp) cc_final: 0.8499 (tpp) REVERT: B 673 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8549 (mtmm) REVERT: B 689 PHE cc_start: 0.8693 (t80) cc_final: 0.8418 (t80) REVERT: B 703 ASN cc_start: 0.7524 (m-40) cc_final: 0.7316 (t0) REVERT: B 893 PHE cc_start: 0.7992 (m-80) cc_final: 0.7041 (m-10) REVERT: B 1057 MET cc_start: 0.8851 (ttp) cc_final: 0.8644 (ptm) REVERT: A 120 ASN cc_start: 0.8297 (t0) cc_final: 0.8067 (m-40) REVERT: A 329 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7337 (mmt90) REVERT: A 353 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8428 (mtmm) REVERT: A 580 GLU cc_start: 0.7973 (tp30) cc_final: 0.7515 (tp30) outliers start: 39 outliers final: 16 residues processed: 212 average time/residue: 0.0982 time to fit residues: 32.6083 Evaluate side-chains 183 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 123 optimal weight: 0.0370 chunk 132 optimal weight: 0.2980 chunk 163 optimal weight: 0.7980 chunk 100 optimal weight: 0.0060 chunk 61 optimal weight: 0.3980 chunk 34 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 137 optimal weight: 0.0060 chunk 109 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 ASN B 777 GLN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101366 restraints weight = 25601.505| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.45 r_work: 0.3418 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14242 Z= 0.113 Angle : 0.613 20.302 19392 Z= 0.295 Chirality : 0.043 0.437 2295 Planarity : 0.003 0.032 2410 Dihedral : 3.963 26.033 1928 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % Rotamer: Outliers : 2.77 % Allowed : 15.81 % Favored : 81.41 % 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: 0.72 (0.20), residues: 1805 helix: 1.61 (0.16), residues: 1011 sheet: -1.04 (0.46), residues: 121 loop : -0.97 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.013 0.001 TYR B 232 PHE 0.020 0.001 PHE B 645 TRP 0.012 0.001 TRP B 649 HIS 0.003 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14228) covalent geometry : angle 0.58001 / 0.29 (19356) SS BOND : bond 0.00297 / 0.14 ( 6) SS BOND : angle 1.62901 / 0.97 ( 12) hydrogen bonds : bond 0.03779 / 2.54 ( 824) hydrogen bonds : angle 4.15115 / 2.99 ( 2382) link_BETA1-4 : bond 0.00710 / 0.36 ( 4) link_BETA1-4 : angle 2.92361 / 1.48 ( 12) link_NAG-ASN : bond 0.01318 / 0.63 ( 4) link_NAG-ASN : angle 7.25516 / 3.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4689 (tpt) cc_final: 0.3966 (tpt) REVERT: B 116 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7750 (pt0) REVERT: B 601 MET cc_start: 0.8648 (tpp) cc_final: 0.8397 (tpp) REVERT: B 673 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8527 (mtmm) REVERT: B 689 PHE cc_start: 0.8638 (t80) cc_final: 0.8382 (t80) REVERT: B 807 MET cc_start: 0.8206 (ttp) cc_final: 0.7786 (ptm) REVERT: B 893 PHE cc_start: 0.8045 (m-80) cc_final: 0.7062 (m-10) REVERT: B 943 MET cc_start: 0.5642 (ptm) cc_final: 0.5413 (ptp) REVERT: A 117 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 329 ARG cc_start: 0.7710 (mmt90) cc_final: 0.7373 (mmt90) REVERT: A 353 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: A 580 GLU cc_start: 0.7977 (tp30) cc_final: 0.7632 (tp30) REVERT: A 646 ILE cc_start: 0.8759 (mt) cc_final: 0.8527 (mt) REVERT: A 873 MET cc_start: 0.7751 (mmm) cc_final: 0.7485 (mpp) REVERT: A 1057 MET cc_start: 0.8465 (ptp) cc_final: 0.8073 (ptp) REVERT: A 1087 VAL cc_start: 0.8296 (t) cc_final: 0.8067 (p) outliers start: 40 outliers final: 21 residues processed: 225 average time/residue: 0.0853 time to fit residues: 30.6061 Evaluate side-chains 195 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 662 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 93 optimal weight: 0.0370 chunk 168 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 561 HIS B 565 ASN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1069 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099854 restraints weight = 25690.886| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.36 r_work: 0.3365 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14242 Z= 0.156 Angle : 0.638 19.606 19392 Z= 0.307 Chirality : 0.045 0.449 2295 Planarity : 0.004 0.031 2410 Dihedral : 3.948 25.872 1928 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 2.91 % Allowed : 17.20 % Favored : 79.89 % 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: 0.74 (0.20), residues: 1805 helix: 1.58 (0.16), residues: 1012 sheet: -1.01 (0.48), residues: 111 loop : -0.89 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.014 0.001 TYR B 105 PHE 0.014 0.001 PHE A 442 TRP 0.011 0.001 TRP B 159 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (14228) covalent geometry : angle 0.60750 / 0.30 (19356) SS BOND : bond 0.00916 / 0.48 ( 6) SS BOND : angle 2.00002 / 1.19 ( 12) hydrogen bonds : bond 0.03866 / 2.61 ( 824) hydrogen bonds : angle 4.17491 / 3.01 ( 2382) link_BETA1-4 : bond 0.00487 / 0.25 ( 4) link_BETA1-4 : angle 2.92724 / 1.50 ( 12) link_NAG-ASN : bond 0.01309 / 0.62 ( 4) link_NAG-ASN : angle 7.04752 / 3.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4686 (tpt) cc_final: 0.4175 (tpt) REVERT: B 116 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7773 (pt0) REVERT: B 673 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8582 (mtmm) REVERT: B 807 MET cc_start: 0.8252 (ttp) cc_final: 0.7838 (ptm) REVERT: B 893 PHE cc_start: 0.8015 (m-80) cc_final: 0.7014 (m-10) REVERT: B 943 MET cc_start: 0.5656 (ptm) cc_final: 0.5401 (ptp) REVERT: A 105 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6360 (p90) REVERT: A 353 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: A 408 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7903 (mm-30) REVERT: A 601 MET cc_start: 0.8358 (tpp) cc_final: 0.7769 (tpp) REVERT: A 646 ILE cc_start: 0.8795 (mt) cc_final: 0.8534 (mt) REVERT: A 871 MET cc_start: 0.8152 (mmp) cc_final: 0.7832 (mmp) outliers start: 42 outliers final: 27 residues processed: 205 average time/residue: 0.0939 time to fit residues: 31.0477 Evaluate side-chains 190 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 565 ASN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099174 restraints weight = 25636.486| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.43 r_work: 0.3384 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14242 Z= 0.127 Angle : 0.619 19.216 19392 Z= 0.297 Chirality : 0.044 0.447 2295 Planarity : 0.003 0.031 2410 Dihedral : 3.967 27.211 1928 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 2.64 % Allowed : 18.17 % Favored : 79.20 % 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: 0.84 (0.20), residues: 1805 helix: 1.67 (0.16), residues: 1008 sheet: -0.98 (0.48), residues: 111 loop : -0.84 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.012 0.001 TYR B 105 PHE 0.027 0.001 PHE B 634 TRP 0.010 0.001 TRP B 159 HIS 0.003 0.000 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14228) covalent geometry : angle 0.58925 / 0.29 (19356) SS BOND : bond 0.00420 / 0.21 ( 6) SS BOND : angle 2.15419 / 1.25 ( 12) hydrogen bonds : bond 0.03746 / 2.53 ( 824) hydrogen bonds : angle 4.15596 / 2.99 ( 2382) link_BETA1-4 : bond 0.00559 / 0.28 ( 4) link_BETA1-4 : angle 2.87152 / 1.47 ( 12) link_NAG-ASN : bond 0.01298 / 0.62 ( 4) link_NAG-ASN : angle 6.85130 / 3.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.4609 (tpt) cc_final: 0.4139 (tpt) REVERT: B 116 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7770 (pt0) REVERT: B 138 MET cc_start: 0.8302 (tpp) cc_final: 0.7956 (tpp) REVERT: B 673 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8543 (mtmm) REVERT: B 689 PHE cc_start: 0.8562 (t80) cc_final: 0.8348 (t80) REVERT: B 807 MET cc_start: 0.8240 (ttp) cc_final: 0.7832 (ptm) REVERT: B 893 PHE cc_start: 0.7984 (m-80) cc_final: 0.7014 (m-10) REVERT: B 943 MET cc_start: 0.5657 (ptm) cc_final: 0.5389 (ptp) REVERT: A 105 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6174 (p90) REVERT: A 280 LEU cc_start: 0.8559 (tp) cc_final: 0.8173 (tt) REVERT: A 353 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8658 (mtmm) REVERT: A 408 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7886 (mm-30) REVERT: A 601 MET cc_start: 0.8349 (tpp) cc_final: 0.7789 (tpp) REVERT: A 646 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8517 (mt) REVERT: A 868 ASP cc_start: 0.7435 (m-30) cc_final: 0.7212 (t0) REVERT: A 871 MET cc_start: 0.8211 (mmp) cc_final: 0.7716 (mmp) REVERT: A 873 MET cc_start: 0.7642 (mmm) cc_final: 0.7436 (mpp) outliers start: 38 outliers final: 27 residues processed: 203 average time/residue: 0.0954 time to fit residues: 31.2326 Evaluate side-chains 201 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1077 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 102 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 613 GLN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.128646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097828 restraints weight = 25653.242| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.39 r_work: 0.3359 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14242 Z= 0.152 Angle : 0.633 18.668 19392 Z= 0.306 Chirality : 0.045 0.450 2295 Planarity : 0.004 0.034 2410 Dihedral : 4.015 26.532 1928 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 2.64 % Allowed : 18.65 % Favored : 78.71 % 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: 0.86 (0.20), residues: 1805 helix: 1.64 (0.16), residues: 1008 sheet: -1.03 (0.47), residues: 111 loop : -0.74 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.013 0.001 TYR A 937 PHE 0.014 0.001 PHE A 137 TRP 0.009 0.001 TRP B 159 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (14228) covalent geometry : angle 0.60508 / 0.30 (19356) SS BOND : bond 0.00475 / 0.24 ( 6) SS BOND : angle 2.24338 / 1.29 ( 12) hydrogen bonds : bond 0.03797 / 2.58 ( 824) hydrogen bonds : angle 4.17963 / 3.01 ( 2382) link_BETA1-4 : bond 0.00359 / 0.18 ( 4) link_BETA1-4 : angle 2.84151 / 1.45 ( 12) link_NAG-ASN : bond 0.01294 / 0.62 ( 4) link_NAG-ASN : angle 6.68496 / 3.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 102 MET cc_start: 0.4569 (tpt) cc_final: 0.4095 (tpt) REVERT: B 116 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7724 (pt0) REVERT: B 117 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8186 (tm-30) REVERT: B 231 MET cc_start: 0.7508 (ttm) cc_final: 0.7184 (ttm) REVERT: B 498 ASP cc_start: 0.8077 (t0) cc_final: 0.7860 (t0) REVERT: B 673 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8552 (mtmm) REVERT: B 807 MET cc_start: 0.8279 (ttp) cc_final: 0.7855 (ptm) REVERT: B 893 PHE cc_start: 0.7974 (m-80) cc_final: 0.7028 (m-10) REVERT: B 943 MET cc_start: 0.5659 (ptm) cc_final: 0.5389 (ptp) REVERT: A 105 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6149 (p90) REVERT: A 117 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7245 (mp0) REVERT: A 280 LEU cc_start: 0.8614 (tp) cc_final: 0.8212 (tt) REVERT: A 353 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8836 (mtmm) REVERT: A 601 MET cc_start: 0.8392 (tpp) cc_final: 0.7846 (tpp) REVERT: A 871 MET cc_start: 0.8305 (mmp) cc_final: 0.7996 (mmp) outliers start: 38 outliers final: 30 residues processed: 204 average time/residue: 0.0970 time to fit residues: 31.4777 Evaluate side-chains 199 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1077 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 70 optimal weight: 0.0770 chunk 86 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 74 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 565 ASN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.130620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100010 restraints weight = 25681.690| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.40 r_work: 0.3396 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14242 Z= 0.122 Angle : 0.626 18.424 19392 Z= 0.299 Chirality : 0.044 0.455 2295 Planarity : 0.003 0.032 2410 Dihedral : 3.964 26.387 1928 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 2.50 % Allowed : 18.59 % Favored : 78.92 % 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: 0.93 (0.20), residues: 1805 helix: 1.73 (0.16), residues: 1009 sheet: -1.06 (0.46), residues: 117 loop : -0.76 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.012 0.001 TYR B 105 PHE 0.027 0.001 PHE B 634 TRP 0.011 0.001 TRP B 649 HIS 0.003 0.000 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14228) covalent geometry : angle 0.59890 / 0.29 (19356) SS BOND : bond 0.00355 / 0.18 ( 6) SS BOND : angle 1.95138 / 1.15 ( 12) hydrogen bonds : bond 0.03637 / 2.46 ( 824) hydrogen bonds : angle 4.11542 / 2.97 ( 2382) link_BETA1-4 : bond 0.00518 / 0.26 ( 4) link_BETA1-4 : angle 2.78618 / 1.42 ( 12) link_NAG-ASN : bond 0.01332 / 0.64 ( 4) link_NAG-ASN : angle 6.53266 / 3.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: B 102 MET cc_start: 0.4598 (tpt) cc_final: 0.4136 (tpt) REVERT: B 116 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7710 (pt0) REVERT: B 117 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8217 (tm-30) REVERT: B 498 ASP cc_start: 0.8051 (t0) cc_final: 0.7806 (t0) REVERT: B 617 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7662 (mtt90) REVERT: B 673 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8559 (mtmm) REVERT: B 807 MET cc_start: 0.8253 (ttp) cc_final: 0.7987 (ptm) REVERT: B 893 PHE cc_start: 0.8005 (m-80) cc_final: 0.7079 (m-10) REVERT: B 943 MET cc_start: 0.5676 (ptm) cc_final: 0.5398 (ptp) REVERT: A 105 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6024 (p90) REVERT: A 280 LEU cc_start: 0.8589 (tp) cc_final: 0.8220 (tt) REVERT: A 353 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: A 357 PHE cc_start: 0.8540 (m-80) cc_final: 0.8188 (t80) REVERT: A 397 TRP cc_start: 0.8625 (m100) cc_final: 0.8304 (m-10) REVERT: A 408 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7897 (mm-30) REVERT: A 601 MET cc_start: 0.8370 (tpp) cc_final: 0.7867 (tpp) REVERT: A 871 MET cc_start: 0.8260 (mmp) cc_final: 0.7912 (mmp) REVERT: A 1055 LEU cc_start: 0.8411 (tp) cc_final: 0.8071 (tt) REVERT: A 1057 MET cc_start: 0.8475 (ptp) cc_final: 0.7510 (pmm) outliers start: 36 outliers final: 29 residues processed: 199 average time/residue: 0.0976 time to fit residues: 30.7599 Evaluate side-chains 200 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1077 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 40 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 123 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** 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 = 0.3978 r_free = 0.3978 target = 0.130680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100311 restraints weight = 25425.118| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.38 r_work: 0.3401 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14242 Z= 0.119 Angle : 0.620 17.980 19392 Z= 0.296 Chirality : 0.044 0.453 2295 Planarity : 0.003 0.031 2410 Dihedral : 3.891 26.625 1928 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.15 % Allowed : 19.07 % Favored : 78.78 % 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: 0.99 (0.20), residues: 1805 helix: 1.77 (0.16), residues: 1012 sheet: -0.91 (0.46), residues: 133 loop : -0.73 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.014 0.001 TYR A 937 PHE 0.023 0.001 PHE B 634 TRP 0.010 0.001 TRP B 649 HIS 0.003 0.000 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14228) covalent geometry : angle 0.59372 / 0.29 (19356) SS BOND : bond 0.00323 / 0.16 ( 6) SS BOND : angle 1.87459 / 1.10 ( 12) hydrogen bonds : bond 0.03570 / 2.42 ( 824) hydrogen bonds : angle 4.05238 / 2.92 ( 2382) link_BETA1-4 : bond 0.00508 / 0.25 ( 4) link_BETA1-4 : angle 2.73442 / 1.40 ( 12) link_NAG-ASN : bond 0.01306 / 0.62 ( 4) link_NAG-ASN : angle 6.38161 / 3.43 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3610 Ramachandran restraints generated. 1805 Oldfield, 0 Emsley, 1805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 102 MET cc_start: 0.4484 (tpt) cc_final: 0.4035 (tpt) REVERT: B 116 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7741 (pt0) REVERT: B 117 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8198 (tm-30) REVERT: B 231 MET cc_start: 0.7551 (ttm) cc_final: 0.7218 (ttm) REVERT: B 498 ASP cc_start: 0.8035 (t0) cc_final: 0.7673 (t70) REVERT: B 673 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8594 (mtmm) REVERT: B 689 PHE cc_start: 0.8535 (t80) cc_final: 0.8334 (t80) REVERT: B 893 PHE cc_start: 0.8010 (m-80) cc_final: 0.7104 (m-10) REVERT: B 943 MET cc_start: 0.5705 (ptm) cc_final: 0.5427 (ptp) REVERT: A 105 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.6158 (p90) REVERT: A 280 LEU cc_start: 0.8605 (tp) cc_final: 0.8234 (tt) REVERT: A 353 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8695 (mtmm) REVERT: A 357 PHE cc_start: 0.8502 (m-80) cc_final: 0.8174 (t80) REVERT: A 397 TRP cc_start: 0.8638 (m100) cc_final: 0.8301 (m-10) REVERT: A 408 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7878 (mm-30) REVERT: A 601 MET cc_start: 0.8368 (tpp) cc_final: 0.7861 (tpp) REVERT: A 871 MET cc_start: 0.8261 (mmp) cc_final: 0.7886 (mmp) REVERT: A 873 MET cc_start: 0.7731 (mmm) cc_final: 0.7447 (mpp) REVERT: A 1055 LEU cc_start: 0.8426 (tp) cc_final: 0.8125 (tt) REVERT: A 1057 MET cc_start: 0.8493 (ptp) cc_final: 0.7527 (pmm) outliers start: 31 outliers final: 26 residues processed: 197 average time/residue: 0.0942 time to fit residues: 30.1263 Evaluate side-chains 194 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 795 CYS Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 924 VAL Chi-restraints excluded: chain B residue 1081 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1077 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 565 ASN ** B1040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.131528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101282 restraints weight = 25738.751| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.35 r_work: 0.3391 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14242 Z= 0.128 Angle : 0.621 17.728 19392 Z= 0.296 Chirality : 0.044 0.459 2295 Planarity : 0.003 0.032 2410 Dihedral : 3.881 26.484 1928 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 2.57 % Allowed : 19.21 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1805 helix: 1.78 (0.16), residues: 1011 sheet: -0.92 (0.46), residues: 132 loop : -0.73 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 820 TYR 0.011 0.001 TYR B 937 PHE 0.023 0.001 PHE B 634 TRP 0.010 0.001 TRP B 649 HIS 0.004 0.000 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14228) covalent geometry : angle 0.59555 / 0.29 (19356) SS BOND : bond 0.00387 / 0.19 ( 6) SS BOND : angle 1.90448 / 1.12 ( 12) hydrogen bonds : bond 0.03582 / 2.42 ( 824) hydrogen bonds : angle 4.04718 / 2.93 ( 2382) link_BETA1-4 : bond 0.00477 / 0.24 ( 4) link_BETA1-4 : angle 2.70298 / 1.38 ( 12) link_NAG-ASN : bond 0.01283 / 0.61 ( 4) link_NAG-ASN : angle 6.28084 / 3.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3262.92 seconds wall clock time: 56 minutes 47.85 seconds (3407.85 seconds total)