Starting phenix.real_space_refine on Fri Aug 7 21:46:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2026/9n6i_49062.cif" } resolution = 2.61 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= 0.005 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 302 5.49 5 S 60 5.16 5 C 14512 2.51 5 N 4466 2.21 5 O 5180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24520 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 840 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 687 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 842 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 712 Classifications: {'peptide': 92} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 816 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 6026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6026 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 23, 'TRANS': 745} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 21, 'ASP:plan': 8, 'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 175 Chain: "K" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6159 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 24, 'TRANS': 756} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 18, 'ASP:plan': 7, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 137 Time building chain proxies: 4.61, per 1000 atoms: 0.19 Number of scatterers: 24520 At special positions: 0 Unit cell: (128.149, 124.998, 211.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 302 15.00 O 5180 8.00 N 4466 7.00 C 14512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 902.2 milliseconds 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4410 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 18 sheets defined 55.3% alpha, 8.6% beta 149 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.532A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 15 removed outlier: 3.629A pdb=" N ALA C 14 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 15 " --> pdb=" O ALA C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 15' Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.375A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.930A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.797A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.505A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.502A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.590A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.542A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.126A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'L' and resid 203 through 211 removed outlier: 3.953A pdb=" N GLU L 209 " --> pdb=" O ASN L 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN L 210 " --> pdb=" O ASN L 206 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR L 211 " --> pdb=" O CYS L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 234 removed outlier: 3.761A pdb=" N GLY L 234 " --> pdb=" O TYR L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 259 removed outlier: 3.663A pdb=" N LEU L 242 " --> pdb=" O GLY L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 283 removed outlier: 3.556A pdb=" N ILE L 267 " --> pdb=" O THR L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 319 removed outlier: 3.661A pdb=" N GLU L 318 " --> pdb=" O ASN L 315 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 319 " --> pdb=" O TYR L 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 315 through 319' Processing helix chain 'L' and resid 324 through 331 Processing helix chain 'L' and resid 331 through 343 removed outlier: 3.774A pdb=" N VAL L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN L 343 " --> pdb=" O GLN L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 351 Processing helix chain 'L' and resid 377 through 393 Processing helix chain 'L' and resid 406 through 421 Processing helix chain 'L' and resid 433 through 435 No H-bonds generated for 'chain 'L' and resid 433 through 435' Processing helix chain 'L' and resid 436 through 448 removed outlier: 3.972A pdb=" N THR L 443 " --> pdb=" O ALA L 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 470 Processing helix chain 'L' and resid 491 through 498 Processing helix chain 'L' and resid 499 through 504 removed outlier: 4.292A pdb=" N SER L 504 " --> pdb=" O ALA L 500 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 520 removed outlier: 4.388A pdb=" N ASN L 520 " --> pdb=" O ARG L 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 531 removed outlier: 3.640A pdb=" N GLU L 527 " --> pdb=" O SER L 523 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 560 removed outlier: 4.225A pdb=" N LEU L 552 " --> pdb=" O ASN L 548 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 590 removed outlier: 3.552A pdb=" N GLU L 580 " --> pdb=" O ASP L 576 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 590 " --> pdb=" O LEU L 586 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 631 Processing helix chain 'L' and resid 633 through 639 Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 662 through 665 Processing helix chain 'L' and resid 668 through 676 removed outlier: 3.699A pdb=" N VAL L 672 " --> pdb=" O ALA L 668 " (cutoff:3.500A) Processing helix chain 'L' and resid 684 through 694 removed outlier: 3.662A pdb=" N ARG L 688 " --> pdb=" O GLU L 684 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER L 694 " --> pdb=" O LEU L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 696 through 710 removed outlier: 3.594A pdb=" N LEU L 700 " --> pdb=" O LYS L 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 720 through 735 Processing helix chain 'L' and resid 746 through 758 Processing helix chain 'L' and resid 794 through 803 removed outlier: 3.964A pdb=" N ASP L 798 " --> pdb=" O ASN L 794 " (cutoff:3.500A) Processing helix chain 'L' and resid 825 through 844 removed outlier: 3.901A pdb=" N VAL L 829 " --> pdb=" O VAL L 825 " (cutoff:3.500A) Processing helix chain 'L' and resid 865 through 874 Processing helix chain 'L' and resid 937 through 954 Processing helix chain 'K' and resid 143 through 147 removed outlier: 3.688A pdb=" N LEU K 147 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 234 Processing helix chain 'K' and resid 238 through 259 Processing helix chain 'K' and resid 263 through 284 removed outlier: 3.741A pdb=" N PHE K 284 " --> pdb=" O GLU K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 319 Processing helix chain 'K' and resid 324 through 331 Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.673A pdb=" N VAL K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN K 343 " --> pdb=" O GLN K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 351 Processing helix chain 'K' and resid 377 through 393 Processing helix chain 'K' and resid 406 through 421 Processing helix chain 'K' and resid 436 through 448 removed outlier: 3.733A pdb=" N THR K 443 " --> pdb=" O ALA K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 471 removed outlier: 3.732A pdb=" N PHE K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 492 through 498 Processing helix chain 'K' and resid 498 through 504 removed outlier: 4.150A pdb=" N SER K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 520 removed outlier: 4.381A pdb=" N ASN K 520 " --> pdb=" O ARG K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 531 removed outlier: 3.543A pdb=" N SER K 531 " --> pdb=" O GLU K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 560 removed outlier: 4.111A pdb=" N LEU K 552 " --> pdb=" O ASN K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 576 through 590 Processing helix chain 'K' and resid 619 through 631 Processing helix chain 'K' and resid 633 through 639 Processing helix chain 'K' and resid 650 through 661 Processing helix chain 'K' and resid 662 through 665 Processing helix chain 'K' and resid 668 through 677 removed outlier: 3.544A pdb=" N VAL K 672 " --> pdb=" O ALA K 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 684 through 694 removed outlier: 4.433A pdb=" N SER K 694 " --> pdb=" O LEU K 690 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 710 removed outlier: 3.912A pdb=" N VAL K 698 " --> pdb=" O SER K 694 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU K 699 " --> pdb=" O GLY K 695 " (cutoff:3.500A) Processing helix chain 'K' and resid 720 through 735 Processing helix chain 'K' and resid 746 through 758 Processing helix chain 'K' and resid 794 through 804 removed outlier: 3.843A pdb=" N ASP K 798 " --> pdb=" O ASN K 794 " (cutoff:3.500A) Processing helix chain 'K' and resid 825 through 844 Processing helix chain 'K' and resid 857 through 873 removed outlier: 3.816A pdb=" N ALA K 862 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY K 863 " --> pdb=" O GLU K 859 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER K 866 " --> pdb=" O ALA K 862 " (cutoff:3.500A) Processing helix chain 'K' and resid 913 through 919 removed outlier: 3.524A pdb=" N LEU K 918 " --> pdb=" O GLY K 914 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS K 919 " --> pdb=" O GLU K 915 " (cutoff:3.500A) Processing helix chain 'K' and resid 937 through 954 removed outlier: 3.631A pdb=" N LYS K 952 " --> pdb=" O GLU K 948 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP K 953 " --> pdb=" O GLN K 949 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.452A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.408A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.031A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.495A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.044A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 179 through 186 removed outlier: 5.342A pdb=" N VAL L 182 " --> pdb=" O LYS L 216 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS L 216 " --> pdb=" O VAL L 182 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN L 184 " --> pdb=" O LEU L 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 287 through 296 removed outlier: 5.750A pdb=" N ILE L 290 " --> pdb=" O LYS L 310 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS L 310 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP L 292 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 453 through 456 removed outlier: 6.578A pdb=" N ILE L 454 " --> pdb=" O LEU L 489 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN L 508 " --> pdb=" O ASN L 536 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N MET L 538 " --> pdb=" O GLN L 508 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET L 510 " --> pdb=" O MET L 538 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE L 540 " --> pdb=" O MET L 510 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL L 512 " --> pdb=" O ILE L 540 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY L 397 " --> pdb=" O LEU L 539 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE L 398 " --> pdb=" O LEU L 595 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 738 through 741 removed outlier: 6.673A pdb=" N GLN L 739 " --> pdb=" O LEU L 768 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N SER L 770 " --> pdb=" O GLN L 739 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU L 741 " --> pdb=" O SER L 770 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL L 714 " --> pdb=" O PHE L 767 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU L 769 " --> pdb=" O VAL L 714 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE L 716 " --> pdb=" O LEU L 769 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR L 610 " --> pdb=" O VAL L 816 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG L 818 " --> pdb=" O THR L 610 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG L 612 " --> pdb=" O ARG L 818 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL L 820 " --> pdb=" O ARG L 612 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU L 614 " --> pdb=" O VAL L 820 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR L 924 " --> pdb=" O GLU L 611 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE L 613 " --> pdb=" O THR L 924 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 179 through 186 removed outlier: 5.325A pdb=" N VAL K 182 " --> pdb=" O LYS K 216 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS K 216 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN K 184 " --> pdb=" O LEU K 214 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 287 through 296 removed outlier: 6.534A pdb=" N LEU K 308 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER K 293 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN K 306 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG K 295 " --> pdb=" O GLN K 304 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN K 304 " --> pdb=" O ARG K 295 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 453 through 456 removed outlier: 6.487A pdb=" N ILE K 454 " --> pdb=" O LEU K 489 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR K 491 " --> pdb=" O ILE K 454 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N TYR K 456 " --> pdb=" O THR K 491 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN K 508 " --> pdb=" O ASN K 536 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N MET K 538 " --> pdb=" O GLN K 508 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET K 510 " --> pdb=" O MET K 538 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE K 540 " --> pdb=" O MET K 510 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL K 512 " --> pdb=" O ILE K 540 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY K 397 " --> pdb=" O LEU K 539 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE K 398 " --> pdb=" O LEU K 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 738 through 741 removed outlier: 6.705A pdb=" N GLN K 739 " --> pdb=" O LEU K 768 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N SER K 770 " --> pdb=" O GLN K 739 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU K 741 " --> pdb=" O SER K 770 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL K 714 " --> pdb=" O PHE K 767 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU K 769 " --> pdb=" O VAL K 714 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE K 716 " --> pdb=" O LEU K 769 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU K 715 " --> pdb=" O VAL K 787 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL K 786 " --> pdb=" O TYR K 817 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU K 819 " --> pdb=" O VAL K 786 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE K 788 " --> pdb=" O LEU K 819 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SER K 821 " --> pdb=" O ILE K 788 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR K 924 " --> pdb=" O GLU K 611 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE K 613 " --> pdb=" O THR K 924 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 926 " --> pdb=" O ILE K 613 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG K 615 " --> pdb=" O TYR K 926 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 382 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 149 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 1.96 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: 5887 1.33 - 1.45: 6589 1.45 - 1.58: 12400 1.58 - 1.70: 602 1.70 - 1.82: 108 Bond restraints: 25586 Sorted by residual: bond pdb=" C3' DC I -49 " pdb=" O3' DC I -49 " ideal model delta sigma weight residual 1.435 1.478 -0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" C5' DC I 37 " pdb=" C4' DC I 37 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.53e+00 bond pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C5' DA I -5 " pdb=" C4' DA I -5 " ideal model delta sigma weight residual 1.512 1.533 -0.021 7.00e-03 2.04e+04 8.61e+00 bond pdb=" C3' DG I -19 " pdb=" C2' DG I -19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.00e+00 ... (remaining 25581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 34569 2.03 - 4.06: 1213 4.06 - 6.08: 76 6.08 - 8.11: 25 8.11 - 10.14: 6 Bond angle restraints: 35889 Sorted by residual: angle pdb=" N GLU L 252 " pdb=" CA GLU L 252 " pdb=" CB GLU L 252 " ideal model delta sigma weight residual 110.40 118.83 -8.43 1.63e+00 3.76e-01 2.67e+01 angle pdb=" O4' DC I -21 " pdb=" C4' DC I -21 " pdb=" C3' DC I -21 " ideal model delta sigma weight residual 106.00 102.93 3.07 6.00e-01 2.78e+00 2.62e+01 angle pdb=" C GLY L 677 " pdb=" N ASP L 678 " pdb=" CA ASP L 678 " ideal model delta sigma weight residual 122.08 129.41 -7.33 1.47e+00 4.63e-01 2.49e+01 angle pdb=" C LYS L 822 " pdb=" N ASP L 823 " pdb=" CA ASP L 823 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" O4' DT I 30 " pdb=" C4' DT I 30 " pdb=" C3' DT I 30 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 ... (remaining 35884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 12650 29.64 - 59.28: 1897 59.28 - 88.92: 62 88.92 - 118.56: 1 118.56 - 148.20: 2 Dihedral angle restraints: 14612 sinusoidal: 7809 harmonic: 6803 Sorted by residual: dihedral pdb=" CA THR K 631 " pdb=" C THR K 631 " pdb=" N LYS K 632 " pdb=" CA LYS K 632 " ideal model delta harmonic sigma weight residual -180.00 -147.57 -32.43 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA THR L 631 " pdb=" C THR L 631 " pdb=" N LYS L 632 " pdb=" CA LYS L 632 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU K 769 " pdb=" C LEU K 769 " pdb=" N SER K 770 " pdb=" CA SER K 770 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 14609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3306 0.062 - 0.124: 646 0.124 - 0.187: 79 0.187 - 0.249: 9 0.249 - 0.311: 1 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CG LEU K 769 " pdb=" CB LEU K 769 " pdb=" CD1 LEU K 769 " pdb=" CD2 LEU K 769 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLU L 252 " pdb=" N GLU L 252 " pdb=" C GLU L 252 " pdb=" CB GLU L 252 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL K 825 " pdb=" CA VAL K 825 " pdb=" CG1 VAL K 825 " pdb=" CG2 VAL K 825 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4038 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO G 80 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO C 80 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET K 437 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO K 438 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 438 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 438 " -0.036 5.00e-02 4.00e+02 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 214 2.60 - 3.17: 18178 3.17 - 3.75: 41931 3.75 - 4.32: 58242 4.32 - 4.90: 87861 Nonbonded interactions: 206426 Sorted by model distance: nonbonded pdb=" NE2 GLN L 410 " pdb=" NH2 ARG L 597 " model vdw 2.023 3.200 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.268 2.496 nonbonded pdb=" O LYS L 627 " pdb=" OG1 THR L 631 " model vdw 2.296 3.040 nonbonded pdb=" N2 DG I -31 " pdb=" O2 DC J 31 " model vdw 2.298 2.496 nonbonded pdb=" O2 DC I -33 " pdb=" N2 DG J 33 " model vdw 2.301 2.496 ... (remaining 206421 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 38 through 135) selection = (chain 'E' and ((resid 38 and (name N or name CA or name C or name O or name CB \ )) or resid 39 through 135)) } ncs_group { reference = (chain 'B' and (resid 15 through 18 or (resid 19 through 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 102)) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 10 through 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 119)) selection = (chain 'G' and (resid 10 through 117 or (resid 118 through 119 and (name N or na \ me CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB \ )) or resid 31 through 120 or (resid 121 and (name N or name CA or name C or nam \ e O )))) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 122 through 849 or resid 864 through 870 or (resid 871 and \ (name N or name CA or name C or name O or name CB )) or resid 872 through 877 o \ r resid 893 through 899 or resid 914 or (resid 915 through 920 and (name N or na \ me CA or name C or name O or name CB )) or resid 921 through 933 or (resid 934 t \ hrough 956 and (name N or name CA or name C or name O or name CB )))) selection = chain 'L' } 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: 2.240 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.640 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.005 0.056 25586 Z= 0.422 Angle : 0.796 10.139 35889 Z= 0.592 Chirality : 0.050 0.311 4041 Planarity : 0.005 0.073 3561 Dihedral : 22.214 148.204 10202 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.79 (0.15), residues: 2294 helix: -1.06 (0.13), residues: 1191 sheet: -0.08 (0.37), residues: 187 loop : -1.41 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 67 TYR 0.033 0.002 TYR F 88 PHE 0.033 0.002 PHE K 767 TRP 0.012 0.001 TRP K 311 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.42 (25586) covalent geometry : angle 0.79554 / 0.59 (35889) hydrogen bonds : bond 0.13219 / 14.42 ( 1288) hydrogen bonds : angle 5.59257 / 7.07 ( 3398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8533 (mmtt) REVERT: D 105 LYS cc_start: 0.9028 (tmmt) cc_final: 0.8708 (tmtt) REVERT: H 102 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7570 (mm-30) REVERT: E 68 GLN cc_start: 0.8911 (tt0) cc_final: 0.8600 (tt0) REVERT: L 876 MET cc_start: 0.5616 (ptm) cc_final: 0.4908 (tpt) REVERT: K 235 GLN cc_start: 0.7532 (tm-30) cc_final: 0.7331 (tm-30) REVERT: K 781 MET cc_start: 0.7379 (tpt) cc_final: 0.6975 (mmt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.8503 time to fit residues: 202.5706 Evaluate side-chains 167 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 258 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 73 ASN A 68 GLN L 428 HIS L 546 GLN K 222 HIS ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083189 restraints weight = 50219.686| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.96 r_work: 0.3142 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 25586 Z= 0.367 Angle : 0.713 8.991 35889 Z= 0.391 Chirality : 0.050 0.257 4041 Planarity : 0.005 0.055 3561 Dihedral : 25.993 158.135 5843 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.11 % Allowed : 9.24 % Favored : 89.65 % 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: -0.51 (0.17), residues: 2294 helix: 0.38 (0.15), residues: 1228 sheet: -0.14 (0.37), residues: 190 loop : -1.35 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 130 TYR 0.015 0.002 TYR K 494 PHE 0.024 0.002 PHE K 471 TRP 0.013 0.002 TRP L 311 HIS 0.005 0.001 HIS K 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.37 (25586) covalent geometry : angle 0.71342 / 0.39 (35889) hydrogen bonds : bond 0.07293 / 8.20 ( 1288) hydrogen bonds : angle 3.96279 / 4.92 ( 3398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (mm) REVERT: E 79 LYS cc_start: 0.9156 (tttp) cc_final: 0.8904 (tttm) REVERT: A 133 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: L 222 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: L 876 MET cc_start: 0.6185 (ptm) cc_final: 0.5060 (tpt) REVERT: K 781 MET cc_start: 0.8245 (tpt) cc_final: 0.7907 (mtp) outliers start: 21 outliers final: 5 residues processed: 174 average time/residue: 0.8803 time to fit residues: 169.2019 Evaluate side-chains 164 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 453 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 215 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 653 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 = 0.4177 r_free = 0.4177 target = 0.131713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085485 restraints weight = 50882.029| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.99 r_work: 0.3207 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25586 Z= 0.139 Angle : 0.552 7.860 35889 Z= 0.314 Chirality : 0.042 0.270 4041 Planarity : 0.003 0.044 3561 Dihedral : 25.955 157.101 5843 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.27 % Allowed : 10.40 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.11 (0.17), residues: 2294 helix: 1.00 (0.15), residues: 1227 sheet: -0.13 (0.36), residues: 199 loop : -1.17 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 683 TYR 0.017 0.001 TYR L 245 PHE 0.012 0.001 PHE K 471 TRP 0.011 0.001 TRP L 311 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (25586) covalent geometry : angle 0.55153 / 0.31 (35889) hydrogen bonds : bond 0.04512 / 4.99 ( 1288) hydrogen bonds : angle 3.63938 / 4.46 ( 3398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8850 (tttm) REVERT: G 116 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8559 (mm) REVERT: H 68 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: E 68 GLN cc_start: 0.9100 (tt0) cc_final: 0.8823 (tt0) REVERT: E 79 LYS cc_start: 0.9125 (tttp) cc_final: 0.8864 (tttm) REVERT: A 133 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: L 222 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: L 652 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8223 (tpp) REVERT: L 876 MET cc_start: 0.6156 (ptm) cc_final: 0.4947 (tpt) REVERT: K 781 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7821 (mtp) outliers start: 24 outliers final: 2 residues processed: 181 average time/residue: 0.9806 time to fit residues: 196.5071 Evaluate side-chains 171 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 652 MET Chi-restraints excluded: chain L residue 733 ILE Chi-restraints excluded: chain K residue 781 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 253 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 14 optimal weight: 50.0000 chunk 244 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 653 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 = 0.4138 r_free = 0.4138 target = 0.129013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082849 restraints weight = 50090.863| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.02 r_work: 0.3127 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 25586 Z= 0.328 Angle : 0.658 8.396 35889 Z= 0.361 Chirality : 0.048 0.290 4041 Planarity : 0.004 0.043 3561 Dihedral : 26.156 160.171 5843 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.54 % Allowed : 12.10 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2294 helix: 0.98 (0.15), residues: 1232 sheet: -0.17 (0.36), residues: 199 loop : -1.22 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 683 TYR 0.018 0.002 TYR K 494 PHE 0.015 0.002 PHE E 67 TRP 0.012 0.002 TRP K 311 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.33 (25586) covalent geometry : angle 0.65848 / 0.36 (35889) hydrogen bonds : bond 0.06979 / 7.84 ( 1288) hydrogen bonds : angle 3.72444 / 4.61 ( 3398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8905 (tttm) REVERT: C 92 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: D 105 LYS cc_start: 0.8951 (tttm) cc_final: 0.8586 (tttm) REVERT: D 113 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9038 (pttm) REVERT: G 116 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 133 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: L 222 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: L 876 MET cc_start: 0.6297 (ptm) cc_final: 0.5045 (tpt) REVERT: K 781 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8128 (mtp) outliers start: 29 outliers final: 11 residues processed: 172 average time/residue: 0.9776 time to fit residues: 186.3753 Evaluate side-chains 175 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 272 MET Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 781 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 28 optimal weight: 50.0000 chunk 238 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 232 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 182 optimal weight: 0.0270 chunk 126 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085381 restraints weight = 50401.013| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.93 r_work: 0.3200 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25586 Z= 0.124 Angle : 0.551 9.306 35889 Z= 0.310 Chirality : 0.042 0.314 4041 Planarity : 0.003 0.059 3561 Dihedral : 26.114 161.043 5843 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.43 % Allowed : 12.90 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.43 (0.17), residues: 2294 helix: 1.29 (0.15), residues: 1232 sheet: -0.04 (0.37), residues: 199 loop : -1.09 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 683 TYR 0.032 0.001 TYR A 41 PHE 0.011 0.001 PHE A 67 TRP 0.013 0.001 TRP L 311 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (25586) covalent geometry : angle 0.55101 / 0.31 (35889) hydrogen bonds : bond 0.04319 / 4.79 ( 1288) hydrogen bonds : angle 3.50889 / 4.29 ( 3398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8835 (tttm) REVERT: B 92 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.7973 (ttp80) REVERT: C 92 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: D 105 LYS cc_start: 0.8928 (tttm) cc_final: 0.8531 (tttm) REVERT: D 113 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9042 (pttm) REVERT: G 116 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8671 (mt) REVERT: E 68 GLN cc_start: 0.9090 (tt0) cc_final: 0.8835 (tt0) REVERT: E 79 LYS cc_start: 0.9093 (tttp) cc_final: 0.8825 (tttm) REVERT: A 133 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: L 222 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.7884 (t-90) REVERT: L 876 MET cc_start: 0.6184 (ptm) cc_final: 0.4998 (tpt) outliers start: 27 outliers final: 6 residues processed: 185 average time/residue: 0.8665 time to fit residues: 177.6591 Evaluate side-chains 173 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 733 ILE Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 790 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 177 optimal weight: 30.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN L 536 ASN K 339 GLN ** K 653 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.129765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083217 restraints weight = 50298.280| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.02 r_work: 0.3153 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25586 Z= 0.227 Angle : 0.582 9.956 35889 Z= 0.326 Chirality : 0.044 0.322 4041 Planarity : 0.003 0.056 3561 Dihedral : 26.075 163.983 5843 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.49 % Allowed : 13.32 % Favored : 85.19 % 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: 0.44 (0.17), residues: 2294 helix: 1.33 (0.15), residues: 1233 sheet: -0.08 (0.36), residues: 199 loop : -1.13 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 683 TYR 0.016 0.001 TYR K 494 PHE 0.015 0.001 PHE A 67 TRP 0.012 0.001 TRP K 311 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (25586) covalent geometry : angle 0.58226 / 0.33 (35889) hydrogen bonds : bond 0.05455 / 6.12 ( 1288) hydrogen bonds : angle 3.54010 / 4.34 ( 3398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8882 (tttm) REVERT: B 92 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7962 (ttp80) REVERT: C 92 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: D 113 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9033 (pttm) REVERT: G 75 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8869 (mttm) REVERT: G 116 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8697 (mt) REVERT: E 79 LYS cc_start: 0.9109 (tttp) cc_final: 0.8850 (tttm) REVERT: A 133 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: L 222 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: L 229 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8250 (t) REVERT: L 876 MET cc_start: 0.6243 (ptm) cc_final: 0.5072 (tpt) REVERT: K 837 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8688 (mmm) outliers start: 28 outliers final: 12 residues processed: 174 average time/residue: 0.9275 time to fit residues: 179.8241 Evaluate side-chains 177 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP Chi-restraints excluded: chain K residue 837 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 233 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 157 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 168 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 653 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 = 0.4168 r_free = 0.4168 target = 0.131109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085398 restraints weight = 50421.535| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.00 r_work: 0.3193 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25586 Z= 0.124 Angle : 0.555 11.543 35889 Z= 0.312 Chirality : 0.042 0.332 4041 Planarity : 0.004 0.104 3561 Dihedral : 26.058 164.057 5843 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.43 % Allowed : 13.54 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.53 (0.17), residues: 2294 helix: 1.40 (0.15), residues: 1232 sheet: -0.05 (0.36), residues: 199 loop : -1.06 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 683 TYR 0.016 0.001 TYR K 494 PHE 0.014 0.001 PHE K 789 TRP 0.013 0.001 TRP L 311 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (25586) covalent geometry : angle 0.55534 / 0.31 (35889) hydrogen bonds : bond 0.04434 / 4.94 ( 1288) hydrogen bonds : angle 3.47969 / 4.25 ( 3398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8839 (tttm) REVERT: B 92 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7980 (ttp80) REVERT: C 92 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: D 105 LYS cc_start: 0.8844 (tttm) cc_final: 0.8525 (tttm) REVERT: D 113 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9022 (pttm) REVERT: G 75 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8817 (mttm) REVERT: G 116 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8690 (mt) REVERT: E 68 GLN cc_start: 0.9087 (tt0) cc_final: 0.8831 (tt0) REVERT: E 79 LYS cc_start: 0.9049 (tttp) cc_final: 0.8787 (tttm) REVERT: A 133 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: L 222 HIS cc_start: 0.8603 (OUTLIER) cc_final: 0.7882 (t-90) REVERT: L 229 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8300 (t) REVERT: L 876 MET cc_start: 0.6187 (ptm) cc_final: 0.5097 (tpt) REVERT: K 837 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8664 (mmm) outliers start: 27 outliers final: 9 residues processed: 177 average time/residue: 0.8256 time to fit residues: 162.6731 Evaluate side-chains 179 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP Chi-restraints excluded: chain K residue 837 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 196 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN K 185 HIS ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.084932 restraints weight = 50390.923| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.05 r_work: 0.3188 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25586 Z= 0.147 Angle : 0.552 11.628 35889 Z= 0.311 Chirality : 0.042 0.344 4041 Planarity : 0.003 0.042 3561 Dihedral : 25.936 166.656 5843 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.43 % Allowed : 14.01 % Favored : 84.55 % 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: 0.64 (0.17), residues: 2294 helix: 1.49 (0.15), residues: 1236 sheet: 0.06 (0.37), residues: 194 loop : -1.05 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 683 TYR 0.015 0.001 TYR K 494 PHE 0.015 0.001 PHE A 67 TRP 0.013 0.001 TRP L 311 HIS 0.006 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (25586) covalent geometry : angle 0.55226 / 0.31 (35889) hydrogen bonds : bond 0.04396 / 4.91 ( 1288) hydrogen bonds : angle 3.41380 / 4.17 ( 3398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8863 (tttm) REVERT: B 92 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: D 113 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9050 (pttm) REVERT: G 75 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8844 (mttm) REVERT: G 116 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8694 (mt) REVERT: E 68 GLN cc_start: 0.9119 (tt0) cc_final: 0.8878 (tt0) REVERT: E 79 LYS cc_start: 0.9065 (tttp) cc_final: 0.8817 (tttm) REVERT: L 222 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7990 (t-90) REVERT: L 229 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8225 (t) REVERT: L 876 MET cc_start: 0.6178 (ptm) cc_final: 0.5100 (tpt) REVERT: K 837 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8631 (mmm) outliers start: 27 outliers final: 9 residues processed: 177 average time/residue: 0.9299 time to fit residues: 183.1551 Evaluate side-chains 178 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP Chi-restraints excluded: chain K residue 837 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 257 optimal weight: 0.0370 chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.128226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.081906 restraints weight = 50373.065| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.99 r_work: 0.3116 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 25586 Z= 0.394 Angle : 0.703 12.392 35889 Z= 0.378 Chirality : 0.051 0.361 4041 Planarity : 0.005 0.046 3561 Dihedral : 26.272 171.272 5843 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.33 % Allowed : 14.54 % Favored : 84.13 % 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: 0.21 (0.17), residues: 2294 helix: 1.09 (0.15), residues: 1248 sheet: -0.11 (0.36), residues: 194 loop : -1.19 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 130 TYR 0.020 0.002 TYR K 494 PHE 0.017 0.002 PHE K 871 TRP 0.012 0.002 TRP K 440 HIS 0.006 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.39 (25586) covalent geometry : angle 0.70274 / 0.38 (35889) hydrogen bonds : bond 0.07497 / 8.45 ( 1288) hydrogen bonds : angle 3.70413 / 4.56 ( 3398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8944 (tttm) REVERT: B 92 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8026 (ttp80) REVERT: D 113 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9039 (pttm) REVERT: G 75 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8914 (mttm) REVERT: G 116 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8773 (mt) REVERT: L 222 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7914 (t-90) REVERT: L 229 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8198 (t) REVERT: L 876 MET cc_start: 0.6360 (ptm) cc_final: 0.5085 (tpt) REVERT: K 837 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (mmm) outliers start: 25 outliers final: 10 residues processed: 173 average time/residue: 0.8727 time to fit residues: 167.9470 Evaluate side-chains 173 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP Chi-restraints excluded: chain K residue 837 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 127 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 653 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 = 0.4162 r_free = 0.4162 target = 0.130376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.084744 restraints weight = 50452.403| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.99 r_work: 0.3177 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25586 Z= 0.148 Angle : 0.586 12.759 35889 Z= 0.324 Chirality : 0.042 0.374 4041 Planarity : 0.003 0.040 3561 Dihedral : 26.195 172.615 5843 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.11 % Allowed : 14.81 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.49 (0.17), residues: 2294 helix: 1.36 (0.15), residues: 1242 sheet: -0.01 (0.37), residues: 194 loop : -1.11 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.030 0.001 TYR A 41 PHE 0.011 0.001 PHE A 67 TRP 0.014 0.001 TRP K 311 HIS 0.005 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (25586) covalent geometry : angle 0.58599 / 0.32 (35889) hydrogen bonds : bond 0.04382 / 4.87 ( 1288) hydrogen bonds : angle 3.49605 / 4.28 ( 3398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: D 113 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9065 (pttm) REVERT: G 116 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8763 (mt) REVERT: E 68 GLN cc_start: 0.9127 (tt0) cc_final: 0.8873 (tt0) REVERT: E 79 LYS cc_start: 0.9079 (tttp) cc_final: 0.8829 (tttm) REVERT: A 133 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: L 222 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.7940 (t-90) REVERT: L 229 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (t) REVERT: L 457 MET cc_start: 0.8785 (pmm) cc_final: 0.8516 (pmt) REVERT: L 876 MET cc_start: 0.6245 (ptm) cc_final: 0.4940 (tpt) REVERT: K 402 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8675 (mt-10) REVERT: K 837 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8688 (mmm) outliers start: 21 outliers final: 9 residues processed: 170 average time/residue: 0.8504 time to fit residues: 160.9352 Evaluate side-chains 173 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP Chi-restraints excluded: chain K residue 837 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 252 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 158 optimal weight: 0.0970 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** K 653 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 = 0.4162 r_free = 0.4162 target = 0.130391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085202 restraints weight = 50625.064| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.02 r_work: 0.3180 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25586 Z= 0.157 Angle : 0.566 12.577 35889 Z= 0.316 Chirality : 0.042 0.374 4041 Planarity : 0.003 0.041 3561 Dihedral : 25.995 172.002 5843 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.96 % Allowed : 15.02 % Favored : 84.02 % 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: 0.61 (0.17), residues: 2294 helix: 1.48 (0.15), residues: 1232 sheet: 0.04 (0.37), residues: 194 loop : -1.08 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 683 TYR 0.017 0.001 TYR L 494 PHE 0.014 0.001 PHE A 67 TRP 0.013 0.001 TRP L 311 HIS 0.004 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (25586) covalent geometry : angle 0.56631 / 0.32 (35889) hydrogen bonds : bond 0.04546 / 5.08 ( 1288) hydrogen bonds : angle 3.44427 / 4.21 ( 3398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12017.05 seconds wall clock time: 204 minutes 0.84 seconds (12240.84 seconds total)