Starting phenix.real_space_refine on Sat Jul 4 23:28:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6i_49062/07_2026/9n6i_49062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6i_49062/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9n6i_49062/07_2026/9n6i_49062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6i_49062/07_2026/9n6i_49062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6i_49062/07_2026/9n6i_49062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6i_49062/07_2026/9n6i_49062.map" } 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-dev-6108/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: 5.31, per 1000 atoms: 0.22 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: 1.98 Conformation dependent library (CDL) restraints added in 969.3 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: 3.44 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: 7.74 Time building geometry restraints manager: 2.66 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: 34577 2.03 - 4.06: 1206 4.06 - 6.08: 75 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.900 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- 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= 0.421 Angle : 0.791 10.139 35889 Z= 0.587 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 0.79100 / 0.59 (35889) hydrogen bonds : bond 0.13219 / 14.34 ( 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 : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 LYS cc_start: 0.8321 (tptt) cc_final: 0.7855 (pmtt) 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: 1.0032 time to fit residues: 238.6413 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 : 0.812 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083334 restraints weight = 50313.459| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.04 r_work: 0.3138 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 25586 Z= 0.362 Angle : 0.695 8.741 35889 Z= 0.385 Chirality : 0.050 0.239 4041 Planarity : 0.005 0.051 3561 Dihedral : 25.946 157.498 5843 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.11 % Allowed : 9.08 % Favored : 89.81 % 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: 0.37 (0.15), residues: 1223 sheet: -0.12 (0.37), residues: 190 loop : -1.33 (0.18), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 130 TYR 0.015 0.002 TYR K 494 PHE 0.022 0.002 PHE K 471 TRP 0.013 0.002 TRP L 311 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.36 (25586) covalent geometry : angle 0.69496 / 0.39 (35889) hydrogen bonds : bond 0.07139 / 7.96 ( 1288) hydrogen bonds : angle 3.98726 / 4.95 ( 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 188 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 116 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8580 (mm) REVERT: E 79 LYS cc_start: 0.9158 (tttp) cc_final: 0.8908 (tttm) REVERT: A 133 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: L 222 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.7761 (t-90) REVERT: L 876 MET cc_start: 0.6176 (ptm) cc_final: 0.4965 (tpt) REVERT: K 276 ARG cc_start: 0.8574 (ttm170) cc_final: 0.8325 (tpp-160) REVERT: K 733 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8854 (mp) REVERT: K 781 MET cc_start: 0.8175 (tpt) cc_final: 0.7802 (mtp) outliers start: 21 outliers final: 5 residues processed: 176 average time/residue: 0.8840 time to fit residues: 172.1140 Evaluate side-chains 167 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 733 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 215 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 150 optimal weight: 0.0030 chunk 220 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.131974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.086956 restraints weight = 50788.556| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.95 r_work: 0.3218 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25586 Z= 0.132 Angle : 0.552 7.205 35889 Z= 0.315 Chirality : 0.042 0.247 4041 Planarity : 0.003 0.051 3561 Dihedral : 25.995 156.662 5843 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.11 % Allowed : 10.51 % Favored : 88.38 % 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: 0.08 (0.17), residues: 2294 helix: 0.95 (0.15), residues: 1223 sheet: -0.09 (0.37), residues: 199 loop : -1.16 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 683 TYR 0.016 0.001 TYR L 245 PHE 0.012 0.001 PHE K 471 TRP 0.011 0.001 TRP L 311 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (25586) covalent geometry : angle 0.55154 / 0.31 (35889) hydrogen bonds : bond 0.04502 / 4.90 ( 1288) hydrogen bonds : angle 3.67231 / 4.49 ( 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 194 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8857 (tttm) REVERT: G 116 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8505 (mm) REVERT: H 68 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 68 GLN cc_start: 0.9088 (tt0) cc_final: 0.8829 (tt0) REVERT: A 133 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: L 222 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7765 (t-90) REVERT: L 876 MET cc_start: 0.6157 (ptm) cc_final: 0.4952 (tpt) REVERT: K 781 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7803 (mtp) outliers start: 21 outliers final: 2 residues processed: 182 average time/residue: 0.9532 time to fit residues: 191.6903 Evaluate side-chains 171 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 21 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 14 optimal weight: 50.0000 chunk 244 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.128724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082796 restraints weight = 50133.717| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.01 r_work: 0.3119 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 25586 Z= 0.379 Angle : 0.672 8.379 35889 Z= 0.370 Chirality : 0.049 0.258 4041 Planarity : 0.005 0.050 3561 Dihedral : 26.226 160.230 5843 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.80 % Allowed : 11.52 % Favored : 86.68 % 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: 0.00 (0.17), residues: 2294 helix: 0.91 (0.15), residues: 1230 sheet: -0.21 (0.36), residues: 199 loop : -1.22 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 683 TYR 0.018 0.002 TYR K 494 PHE 0.016 0.002 PHE A 104 TRP 0.012 0.002 TRP K 311 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00817 / 0.38 (25586) covalent geometry : angle 0.67192 / 0.37 (35889) hydrogen bonds : bond 0.07543 / 8.42 ( 1288) hydrogen bonds : angle 3.80042 / 4.69 ( 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 197 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8928 (tttm) REVERT: C 92 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8532 (mt-10) REVERT: D 113 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9050 (pttm) REVERT: G 116 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8659 (mt) REVERT: A 133 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: L 222 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7802 (t-90) REVERT: L 876 MET cc_start: 0.6315 (ptm) cc_final: 0.5058 (tpt) REVERT: K 652 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8598 (ttp) REVERT: K 781 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8179 (mtp) outliers start: 34 outliers final: 12 residues processed: 175 average time/residue: 0.8917 time to fit residues: 172.3069 Evaluate side-chains 177 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 31 LYS 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 652 MET 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: 0.8980 chunk 239 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 232 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4172 r_free = 0.4172 target = 0.131366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085857 restraints weight = 50462.454| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.93 r_work: 0.3205 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25586 Z= 0.134 Angle : 0.546 9.272 35889 Z= 0.310 Chirality : 0.042 0.288 4041 Planarity : 0.003 0.053 3561 Dihedral : 26.186 161.211 5843 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.49 % Allowed : 12.90 % Favored : 85.62 % 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: 0.40 (0.17), residues: 2294 helix: 1.27 (0.15), residues: 1230 sheet: -0.11 (0.36), residues: 199 loop : -1.08 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 683 TYR 0.033 0.001 TYR A 41 PHE 0.013 0.001 PHE A 67 TRP 0.012 0.001 TRP L 311 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (25586) covalent geometry : angle 0.54635 / 0.31 (35889) hydrogen bonds : bond 0.04328 / 4.74 ( 1288) hydrogen bonds : angle 3.52257 / 4.30 ( 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 197 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 75 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8857 (mttm) REVERT: G 116 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mt) REVERT: E 68 GLN cc_start: 0.9112 (tt0) cc_final: 0.8859 (tt0) REVERT: L 222 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7883 (t-90) REVERT: L 876 MET cc_start: 0.6197 (ptm) cc_final: 0.5020 (tpt) outliers start: 28 outliers final: 5 residues processed: 181 average time/residue: 0.9169 time to fit residues: 183.4200 Evaluate side-chains 169 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 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 L residue 222 HIS 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: 0.9990 chunk 99 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN L 536 ASN ** 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 = 0.4155 r_free = 0.4155 target = 0.129991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083985 restraints weight = 50145.174| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.07 r_work: 0.3159 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25586 Z= 0.199 Angle : 0.561 10.029 35889 Z= 0.318 Chirality : 0.043 0.296 4041 Planarity : 0.003 0.054 3561 Dihedral : 26.105 164.028 5843 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.49 % Allowed : 13.48 % Favored : 85.03 % 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: -0.10 (0.36), residues: 199 loop : -1.11 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 L 311 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (25586) covalent geometry : angle 0.56127 / 0.32 (35889) hydrogen bonds : bond 0.05154 / 5.71 ( 1288) hydrogen bonds : angle 3.51720 / 4.30 ( 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 189 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: C 92 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8695 (mt-10) REVERT: G 75 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8948 (mttm) REVERT: G 116 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8702 (mt) REVERT: E 68 GLN cc_start: 0.9109 (tt0) cc_final: 0.8856 (tt0) REVERT: A 133 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: L 222 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: L 229 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8196 (t) REVERT: L 876 MET cc_start: 0.6236 (ptm) cc_final: 0.5091 (tpt) REVERT: K 837 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8718 (mmm) outliers start: 28 outliers final: 11 residues processed: 176 average time/residue: 0.9207 time to fit residues: 179.6060 Evaluate side-chains 177 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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: 0.1980 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 230 optimal weight: 0.0070 chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** 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 = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085367 restraints weight = 50214.817| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.08 r_work: 0.3194 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25586 Z= 0.120 Angle : 0.546 12.372 35889 Z= 0.310 Chirality : 0.042 0.300 4041 Planarity : 0.003 0.110 3561 Dihedral : 26.104 164.027 5843 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.38 % Allowed : 13.91 % Favored : 84.71 % 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: 0.57 (0.17), residues: 2294 helix: 1.45 (0.15), residues: 1232 sheet: -0.09 (0.36), residues: 199 loop : -1.06 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG K 683 TYR 0.017 0.001 TYR K 494 PHE 0.013 0.001 PHE A 67 TRP 0.013 0.001 TRP K 311 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (25586) covalent geometry : angle 0.54607 / 0.31 (35889) hydrogen bonds : bond 0.04499 / 4.96 ( 1288) hydrogen bonds : angle 3.49047 / 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 189 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.7972 (ttp80) REVERT: C 92 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8686 (mt-10) REVERT: G 75 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8819 (mttm) REVERT: G 116 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (mt) REVERT: E 68 GLN cc_start: 0.9099 (tt0) cc_final: 0.8838 (tt0) REVERT: A 133 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: L 222 HIS cc_start: 0.8611 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: L 229 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8200 (t) REVERT: L 876 MET cc_start: 0.6189 (ptm) cc_final: 0.5117 (tpt) REVERT: K 437 MET cc_start: 0.9099 (tpp) cc_final: 0.8894 (tpp) REVERT: K 457 MET cc_start: 0.8668 (ptt) cc_final: 0.8461 (ptt) REVERT: K 683 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7476 (tpt90) REVERT: K 837 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8690 (mmm) outliers start: 26 outliers final: 10 residues processed: 176 average time/residue: 0.9377 time to fit residues: 182.9691 Evaluate side-chains 176 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 G residue 75 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 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 272 MET Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 538 MET 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: 0.7980 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 255 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 103 optimal weight: 0.0010 chunk 110 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.131334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.085676 restraints weight = 50241.381| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.04 r_work: 0.3200 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 25586 Z= 0.124 Angle : 0.539 11.721 35889 Z= 0.308 Chirality : 0.041 0.308 4041 Planarity : 0.003 0.055 3561 Dihedral : 26.065 164.861 5843 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.11 % Allowed : 14.33 % 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: 0.62 (0.17), residues: 2294 helix: 1.50 (0.15), residues: 1228 sheet: 0.02 (0.37), residues: 194 loop : -1.07 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 683 TYR 0.015 0.001 TYR K 494 PHE 0.019 0.001 PHE K 789 TRP 0.013 0.001 TRP L 311 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (25586) covalent geometry : angle 0.53948 / 0.31 (35889) hydrogen bonds : bond 0.04295 / 4.70 ( 1288) hydrogen bonds : angle 3.44797 / 4.19 ( 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 182 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: C 92 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8684 (mt-10) REVERT: G 75 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8884 (mttm) REVERT: G 116 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8691 (mt) REVERT: E 68 GLN cc_start: 0.9107 (tt0) cc_final: 0.8881 (tt0) REVERT: A 133 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: L 222 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7948 (t-90) REVERT: L 229 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (t) REVERT: L 837 MET cc_start: 0.9037 (mmm) cc_final: 0.8834 (mtp) REVERT: L 876 MET cc_start: 0.6183 (ptm) cc_final: 0.5104 (tpt) outliers start: 21 outliers final: 8 residues processed: 171 average time/residue: 0.9756 time to fit residues: 184.6811 Evaluate side-chains 173 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 G residue 75 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 257 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.128413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081193 restraints weight = 50302.564| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.18 r_work: 0.3112 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 25586 Z= 0.374 Angle : 0.672 11.896 35889 Z= 0.367 Chirality : 0.049 0.324 4041 Planarity : 0.004 0.044 3561 Dihedral : 26.311 170.101 5843 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.43 % Allowed : 14.44 % 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: 0.25 (0.17), residues: 2294 helix: 1.13 (0.15), residues: 1248 sheet: -0.08 (0.37), residues: 194 loop : -1.19 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 683 TYR 0.019 0.002 TYR K 494 PHE 0.016 0.002 PHE K 871 TRP 0.012 0.002 TRP K 440 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.37 (25586) covalent geometry : angle 0.67204 / 0.37 (35889) hydrogen bonds : bond 0.07157 / 8.00 ( 1288) hydrogen bonds : angle 3.68021 / 4.50 ( 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 183 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: G 75 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8979 (mttm) REVERT: G 116 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 133 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: L 222 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.7913 (t-90) REVERT: L 229 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8180 (t) REVERT: L 876 MET cc_start: 0.6306 (ptm) cc_final: 0.5004 (tpt) outliers start: 27 outliers final: 11 residues processed: 172 average time/residue: 0.9269 time to fit residues: 177.6186 Evaluate side-chains 173 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 G residue 75 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 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 453 CYS Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 714 VAL Chi-restraints excluded: chain K residue 790 ASP 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: 0.9990 chunk 110 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 176 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084794 restraints weight = 50285.519| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25586 Z= 0.151 Angle : 0.566 12.279 35889 Z= 0.317 Chirality : 0.042 0.341 4041 Planarity : 0.003 0.051 3561 Dihedral : 26.264 171.646 5843 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.85 % Allowed : 15.13 % Favored : 84.02 % 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: 0.51 (0.17), residues: 2294 helix: 1.38 (0.15), residues: 1236 sheet: 0.01 (0.37), residues: 194 loop : -1.11 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 683 TYR 0.027 0.001 TYR A 41 PHE 0.012 0.001 PHE K 789 TRP 0.014 0.001 TRP L 311 HIS 0.005 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (25586) covalent geometry : angle 0.56566 / 0.32 (35889) hydrogen bonds : bond 0.04401 / 4.83 ( 1288) hydrogen bonds : angle 3.50729 / 4.27 ( 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: 16 poor density : 162 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7958 (ttp80) REVERT: D 105 LYS cc_start: 0.8857 (tttm) cc_final: 0.8537 (tttm) REVERT: G 116 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8760 (mt) REVERT: E 68 GLN cc_start: 0.9113 (tt0) cc_final: 0.8864 (tt0) REVERT: L 222 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7942 (t-90) REVERT: L 229 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8169 (t) REVERT: L 876 MET cc_start: 0.6218 (ptm) cc_final: 0.4983 (tpt) outliers start: 16 outliers final: 7 residues processed: 171 average time/residue: 0.9256 time to fit residues: 175.2128 Evaluate side-chains 171 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 G residue 116 LEU Chi-restraints excluded: chain E 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 714 VAL Chi-restraints excluded: chain K residue 790 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 252 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.130608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.085349 restraints weight = 50562.760| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.02 r_work: 0.3174 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25586 Z= 0.164 Angle : 0.563 12.526 35889 Z= 0.318 Chirality : 0.042 0.341 4041 Planarity : 0.003 0.043 3561 Dihedral : 26.098 171.780 5843 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.64 % Allowed : 15.45 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2294 helix: 1.47 (0.15), residues: 1229 sheet: 0.05 (0.37), residues: 194 loop : -1.09 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 683 TYR 0.018 0.001 TYR A 41 PHE 0.015 0.001 PHE A 67 TRP 0.012 0.001 TRP L 311 HIS 0.004 0.001 HIS K 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (25586) covalent geometry : angle 0.56297 / 0.32 (35889) hydrogen bonds : bond 0.04626 / 5.10 ( 1288) hydrogen bonds : angle 3.46813 / 4.23 ( 3398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12410.25 seconds wall clock time: 211 minutes 7.70 seconds (12667.70 seconds total)