Starting phenix.real_space_refine on Mon Aug 25 00:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6i_49062/08_2025/9n6i_49062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6i_49062/08_2025/9n6i_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_49062/08_2025/9n6i_49062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2025/9n6i_49062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2025/9n6i_49062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6i_49062/08_2025/9n6i_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-2.0-5787/lib/python3.9/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: 6.38, per 1000 atoms: 0.26 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.98 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: 7.28 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=" N ASP K 279 " pdb=" CA ASP K 279 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.26e-02 6.30e+03 5.87e+00 bond pdb=" N MET K 272 " pdb=" CA MET K 272 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.16e-02 7.43e+03 4.98e+00 bond pdb=" N ASP K 271 " pdb=" CA ASP K 271 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" N GLU K 273 " pdb=" CA GLU K 273 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.25e-02 6.40e+03 4.71e+00 bond pdb=" N GLU K 275 " pdb=" CA GLU K 275 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.21e-02 6.83e+03 4.42e+00 ... (remaining 25581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 34974 2.03 - 4.06: 812 4.06 - 6.08: 72 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=" 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=" C ILE L 251 " pdb=" N GLU L 252 " pdb=" CA GLU L 252 " ideal model delta sigma weight residual 121.14 113.58 7.56 1.75e+00 3.27e-01 1.87e+01 angle pdb=" N GLU E 97 " pdb=" CA GLU E 97 " pdb=" CB GLU E 97 " ideal model delta sigma weight residual 110.28 116.63 -6.35 1.55e+00 4.16e-01 1.68e+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: 3471 0.062 - 0.124: 490 0.124 - 0.187: 71 0.187 - 0.249: 8 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.490 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.004 0.056 25586 Z= 0.196 Angle : 0.710 10.139 35889 Z= 0.407 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00409 (25586) covalent geometry : angle 0.71040 (35889) hydrogen bonds : bond 0.13219 ( 1288) hydrogen bonds : angle 5.59257 ( 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 : 0.932 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: 0.9182 time to fit residues: 217.4446 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 : 0.832 ------------------------------------------------------------------------------- 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: 1.9990 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: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN A 68 GLN L 428 HIS L 546 GLN L 800 GLN K 222 HIS ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.129375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083661 restraints weight = 50337.958| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.96 r_work: 0.3144 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 25586 Z= 0.373 Angle : 0.625 7.630 35889 Z= 0.354 Chirality : 0.045 0.194 4041 Planarity : 0.005 0.049 3561 Dihedral : 25.644 157.564 5843 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.22 % Allowed : 8.97 % 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 aren not related in a simple way. whole: -0.43 (0.17), residues: 2294 helix: 0.44 (0.15), residues: 1228 sheet: -0.09 (0.37), residues: 190 loop : -1.30 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 834 TYR 0.016 0.002 TYR K 494 PHE 0.025 0.002 PHE K 471 TRP 0.013 0.002 TRP K 440 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00842 (25586) covalent geometry : angle 0.62525 (35889) hydrogen bonds : bond 0.06418 ( 1288) hydrogen bonds : angle 3.85927 ( 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 190 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ARG cc_start: 0.8424 (ptt90) cc_final: 0.8218 (mtm180) REVERT: B 59 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8871 (tttm) REVERT: G 116 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8641 (mt) REVERT: E 79 LYS cc_start: 0.9155 (tttp) cc_final: 0.8901 (tttm) REVERT: A 133 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: L 222 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7760 (t-90) REVERT: L 876 MET cc_start: 0.6301 (ptm) cc_final: 0.4946 (tpt) REVERT: K 781 MET cc_start: 0.8269 (tpt) cc_final: 0.7949 (mtp) outliers start: 23 outliers final: 5 residues processed: 177 average time/residue: 0.8590 time to fit residues: 167.3894 Evaluate side-chains 164 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU 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 776 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 215 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4163 r_free = 0.4163 target = 0.130787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085693 restraints weight = 50604.974| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.95 r_work: 0.3182 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25586 Z= 0.199 Angle : 0.525 7.307 35889 Z= 0.302 Chirality : 0.038 0.145 4041 Planarity : 0.003 0.051 3561 Dihedral : 25.520 155.180 5843 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.11 % Allowed : 10.67 % Favored : 88.22 % 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 aren not related in a simple way. whole: 0.17 (0.17), residues: 2294 helix: 1.04 (0.15), residues: 1230 sheet: -0.05 (0.37), residues: 199 loop : -1.16 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 683 TYR 0.015 0.001 TYR K 494 PHE 0.015 0.001 PHE A 67 TRP 0.012 0.001 TRP L 311 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00445 (25586) covalent geometry : angle 0.52503 (35889) hydrogen bonds : bond 0.04433 ( 1288) hydrogen bonds : angle 3.54743 ( 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 : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8856 (tttm) REVERT: G 116 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8647 (mt) REVERT: H 31 LYS cc_start: 0.8302 (mppt) cc_final: 0.7995 (mppt) REVERT: E 68 GLN cc_start: 0.9102 (tt0) cc_final: 0.8828 (tt0) REVERT: E 79 LYS cc_start: 0.9145 (tttp) cc_final: 0.8847 (tttm) REVERT: A 133 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: L 222 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7887 (t-90) REVERT: L 876 MET cc_start: 0.6225 (ptm) cc_final: 0.5121 (tpt) REVERT: K 781 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7897 (mtp) outliers start: 21 outliers final: 4 residues processed: 181 average time/residue: 0.8825 time to fit residues: 176.4588 Evaluate side-chains 169 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 48 ASP Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 776 LEU 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: 1.9990 chunk 124 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4143 r_free = 0.4143 target = 0.129342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.083811 restraints weight = 50272.644| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.01 r_work: 0.3142 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 25586 Z= 0.297 Angle : 0.565 8.241 35889 Z= 0.323 Chirality : 0.042 0.185 4041 Planarity : 0.004 0.046 3561 Dihedral : 25.649 158.713 5843 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.49 % Allowed : 11.89 % Favored : 86.62 % 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 aren not related in a simple way. whole: 0.25 (0.17), residues: 2294 helix: 1.14 (0.15), residues: 1233 sheet: -0.07 (0.36), residues: 199 loop : -1.19 (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 0.011 0.001 TRP K 311 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00670 (25586) covalent geometry : angle 0.56546 (35889) hydrogen bonds : bond 0.05408 ( 1288) hydrogen bonds : angle 3.56377 ( 3398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4588 Ramachandran restraints generated. 2294 Oldfield, 0 Emsley, 2294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8851 (tttm) REVERT: G 116 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8761 (mt) REVERT: H 31 LYS cc_start: 0.8305 (mppt) cc_final: 0.8072 (mppt) REVERT: A 133 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: L 222 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.7892 (t-90) REVERT: L 876 MET cc_start: 0.6283 (ptm) cc_final: 0.5168 (tpt) outliers start: 28 outliers final: 10 residues processed: 173 average time/residue: 0.8066 time to fit residues: 154.4565 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 : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain K residue 470 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 28 optimal weight: 10.0000 chunk 238 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085293 restraints weight = 50141.890| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.07 r_work: 0.3189 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25586 Z= 0.152 Angle : 0.522 9.370 35889 Z= 0.301 Chirality : 0.038 0.138 4041 Planarity : 0.003 0.089 3561 Dihedral : 25.657 158.258 5843 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.38 % Allowed : 12.58 % Favored : 86.04 % 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 aren not related in a simple way. whole: 0.45 (0.17), residues: 2294 helix: 1.30 (0.15), residues: 1234 sheet: 0.04 (0.37), residues: 194 loop : -1.09 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 683 TYR 0.014 0.001 TYR K 494 PHE 0.012 0.001 PHE K 877 TRP 0.012 0.001 TRP L 311 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (25586) covalent geometry : angle 0.52153 (35889) hydrogen bonds : bond 0.04401 ( 1288) hydrogen bonds : angle 3.47038 ( 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 194 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8853 (tttm) REVERT: G 116 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8746 (mt) REVERT: H 31 LYS cc_start: 0.8198 (mppt) cc_final: 0.7979 (mppt) REVERT: E 68 GLN cc_start: 0.9084 (tt0) cc_final: 0.8837 (tt0) REVERT: A 133 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: L 222 HIS cc_start: 0.8598 (OUTLIER) cc_final: 0.7896 (t-90) REVERT: L 275 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8747 (tp30) REVERT: L 876 MET cc_start: 0.6325 (ptm) cc_final: 0.5231 (tpt) outliers start: 26 outliers final: 11 residues processed: 183 average time/residue: 0.9316 time to fit residues: 188.7431 Evaluate side-chains 177 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 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 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 723 MET Chi-restraints excluded: chain L residue 776 LEU Chi-restraints excluded: chain L residue 781 MET Chi-restraints excluded: chain K residue 470 GLU Chi-restraints excluded: chain K residue 790 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 176 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN K 339 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.129912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083994 restraints weight = 50275.459| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.15 r_work: 0.3169 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25586 Z= 0.215 Angle : 0.523 10.255 35889 Z= 0.301 Chirality : 0.039 0.130 4041 Planarity : 0.003 0.042 3561 Dihedral : 25.547 161.281 5843 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 12.90 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.17), residues: 2294 helix: 1.42 (0.15), residues: 1235 sheet: 0.06 (0.37), residues: 194 loop : -1.09 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 683 TYR 0.015 0.001 TYR K 494 PHE 0.013 0.001 PHE A 67 TRP 0.012 0.001 TRP K 311 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00482 (25586) covalent geometry : angle 0.52277 (35889) hydrogen bonds : bond 0.04595 ( 1288) hydrogen bonds : angle 3.41267 ( 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 194 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8865 (tttm) REVERT: B 92 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8035 (ttp80) REVERT: G 116 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8746 (mt) REVERT: H 31 LYS cc_start: 0.8252 (mppt) cc_final: 0.8022 (mppt) REVERT: H 68 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: E 68 GLN cc_start: 0.9130 (tt0) cc_final: 0.8866 (tt0) REVERT: A 133 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: L 222 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: L 229 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8219 (t) REVERT: L 252 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8245 (pp20) REVERT: L 876 MET cc_start: 0.6311 (ptm) cc_final: 0.5220 (tpt) REVERT: K 402 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8675 (mt-10) outliers start: 29 outliers final: 11 residues processed: 181 average time/residue: 0.8673 time to fit residues: 174.1175 Evaluate side-chains 181 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU 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 125 THR Chi-restraints excluded: chain L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 723 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 233 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.084655 restraints weight = 50199.647| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.17 r_work: 0.3186 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25586 Z= 0.161 Angle : 0.517 11.423 35889 Z= 0.298 Chirality : 0.037 0.167 4041 Planarity : 0.003 0.042 3561 Dihedral : 25.536 161.669 5843 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.33 % Allowed : 13.54 % Favored : 85.14 % 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 aren not related in a simple way. whole: 0.63 (0.17), residues: 2294 helix: 1.48 (0.15), residues: 1237 sheet: 0.06 (0.37), residues: 194 loop : -1.07 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 683 TYR 0.017 0.001 TYR A 41 PHE 0.012 0.001 PHE A 67 TRP 0.012 0.001 TRP L 311 HIS 0.006 0.001 HIS K 222 Details of bonding type rmsd covalent geometry : bond 0.00358 (25586) covalent geometry : angle 0.51662 (35889) hydrogen bonds : bond 0.04244 ( 1288) hydrogen bonds : angle 3.38013 ( 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 187 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8861 (tttm) REVERT: B 92 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8003 (ttp80) REVERT: G 116 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8745 (mt) REVERT: H 31 LYS cc_start: 0.8199 (mppt) cc_final: 0.7984 (mppt) REVERT: H 68 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: E 68 GLN cc_start: 0.9118 (tt0) cc_final: 0.8890 (tt0) REVERT: L 222 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.7976 (t-90) REVERT: L 229 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8205 (t) REVERT: L 252 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: L 275 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8746 (tp30) REVERT: L 876 MET cc_start: 0.6287 (ptm) cc_final: 0.5221 (tpt) REVERT: K 402 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8668 (mt-10) outliers start: 25 outliers final: 11 residues processed: 177 average time/residue: 0.8438 time to fit residues: 166.0919 Evaluate side-chains 179 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU 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 L residue 222 HIS Chi-restraints excluded: chain L residue 229 THR Chi-restraints excluded: chain L residue 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 723 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 196 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 50.0000 chunk 8 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN A 68 GLN K 185 HIS ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.086157 restraints weight = 50169.700| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.93 r_work: 0.3204 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25586 Z= 0.153 Angle : 0.508 11.782 35889 Z= 0.293 Chirality : 0.037 0.162 4041 Planarity : 0.003 0.042 3561 Dihedral : 25.442 162.482 5843 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.38 % Allowed : 13.80 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.17), residues: 2294 helix: 1.58 (0.15), residues: 1229 sheet: 0.07 (0.37), residues: 196 loop : -1.07 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 341 TYR 0.016 0.001 TYR L 494 PHE 0.012 0.001 PHE A 67 TRP 0.013 0.001 TRP L 311 HIS 0.004 0.001 HIS K 222 Details of bonding type rmsd covalent geometry : bond 0.00339 (25586) covalent geometry : angle 0.50823 (35889) hydrogen bonds : bond 0.03988 ( 1288) hydrogen bonds : angle 3.34655 ( 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 187 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8853 (tttm) REVERT: B 92 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8023 (ttp80) REVERT: G 116 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8696 (mt) REVERT: H 31 LYS cc_start: 0.8210 (mppt) cc_final: 0.7996 (mppt) REVERT: H 68 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: E 68 GLN cc_start: 0.9123 (tt0) cc_final: 0.8876 (tt0) REVERT: A 133 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: L 222 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.7977 (t-90) REVERT: L 229 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8254 (t) REVERT: L 252 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (pp20) REVERT: L 457 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8470 (pmt) REVERT: L 876 MET cc_start: 0.6207 (ptm) cc_final: 0.5203 (tpt) outliers start: 26 outliers final: 11 residues processed: 175 average time/residue: 0.8963 time to fit residues: 173.7760 Evaluate side-chains 181 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 113 LYS 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 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 723 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: 7.9990 chunk 162 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 251 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4149 r_free = 0.4149 target = 0.129443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083400 restraints weight = 50209.579| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.08 r_work: 0.3155 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25586 Z= 0.253 Angle : 0.548 13.618 35889 Z= 0.312 Chirality : 0.040 0.160 4041 Planarity : 0.003 0.041 3561 Dihedral : 25.574 165.726 5843 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.43 % Allowed : 13.96 % Favored : 84.61 % 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 aren not related in a simple way. whole: 0.61 (0.17), residues: 2294 helix: 1.48 (0.15), residues: 1233 sheet: 0.09 (0.37), residues: 194 loop : -1.09 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 130 TYR 0.017 0.001 TYR L 494 PHE 0.013 0.001 PHE A 67 TRP 0.010 0.001 TRP K 311 HIS 0.004 0.001 HIS K 222 Details of bonding type rmsd covalent geometry : bond 0.00572 (25586) covalent geometry : angle 0.54807 (35889) hydrogen bonds : bond 0.04819 ( 1288) hydrogen bonds : angle 3.43189 ( 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 186 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8894 (tttm) REVERT: B 92 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8041 (ttp80) REVERT: G 116 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (mt) REVERT: H 31 LYS cc_start: 0.8251 (mppt) cc_final: 0.8008 (mppt) REVERT: H 68 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: L 222 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7994 (t-90) REVERT: L 229 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8200 (t) REVERT: L 252 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: L 457 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (pmt) REVERT: L 876 MET cc_start: 0.6256 (ptm) cc_final: 0.5233 (tpt) REVERT: K 402 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8662 (mt-10) REVERT: K 837 MET cc_start: 0.8765 (tpp) cc_final: 0.8540 (mmm) outliers start: 27 outliers final: 12 residues processed: 175 average time/residue: 0.7793 time to fit residues: 151.3223 Evaluate side-chains 178 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU 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 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 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 723 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 127 optimal weight: 0.0010 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 176 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084850 restraints weight = 50192.940| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.12 r_work: 0.3187 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25586 Z= 0.148 Angle : 0.535 14.487 35889 Z= 0.304 Chirality : 0.038 0.177 4041 Planarity : 0.003 0.041 3561 Dihedral : 25.586 165.398 5843 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.22 % Allowed : 14.38 % Favored : 84.39 % 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 aren not related in a simple way. whole: 0.68 (0.17), residues: 2294 helix: 1.55 (0.15), residues: 1230 sheet: 0.10 (0.37), residues: 194 loop : -1.06 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 499 TYR 0.017 0.001 TYR L 494 PHE 0.018 0.001 PHE K 789 TRP 0.013 0.001 TRP L 311 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00325 (25586) covalent geometry : angle 0.53516 (35889) hydrogen bonds : bond 0.04380 ( 1288) hydrogen bonds : angle 3.39347 ( 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 186 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8873 (tttm) REVERT: B 92 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: G 116 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8757 (mt) REVERT: H 31 LYS cc_start: 0.8177 (mppt) cc_final: 0.7968 (mppt) REVERT: H 68 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: E 68 GLN cc_start: 0.9085 (tt0) cc_final: 0.8830 (tt0) REVERT: A 133 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: L 222 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.7945 (t-90) REVERT: L 229 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8190 (t) REVERT: L 252 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8200 (pp20) REVERT: L 275 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8745 (tp30) REVERT: L 876 MET cc_start: 0.6303 (ptm) cc_final: 0.5247 (tpt) REVERT: K 402 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8678 (mt-10) REVERT: K 837 MET cc_start: 0.8734 (tpp) cc_final: 0.8507 (mmm) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.7980 time to fit residues: 156.5926 Evaluate side-chains 179 residues out of total 2047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 113 LYS 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 252 GLU Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 723 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 252 optimal weight: 0.0040 chunk 161 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 256 optimal weight: 1.9990 chunk 182 optimal weight: 0.0980 chunk 189 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.5832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.131006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085661 restraints weight = 50611.001| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3194 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25586 Z= 0.145 Angle : 0.529 14.296 35889 Z= 0.300 Chirality : 0.037 0.148 4041 Planarity : 0.003 0.042 3561 Dihedral : 25.543 165.496 5843 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.01 % Allowed : 14.54 % Favored : 84.45 % 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 aren not related in a simple way. whole: 0.73 (0.18), residues: 2294 helix: 1.60 (0.15), residues: 1230 sheet: 0.06 (0.37), residues: 196 loop : -1.05 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 499 TYR 0.018 0.001 TYR L 494 PHE 0.017 0.001 PHE K 789 TRP 0.013 0.001 TRP L 311 HIS 0.003 0.001 HIS K 222 Details of bonding type rmsd covalent geometry : bond 0.00318 (25586) covalent geometry : angle 0.52917 (35889) hydrogen bonds : bond 0.04062 ( 1288) hydrogen bonds : angle 3.37523 ( 3398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11960.00 seconds wall clock time: 202 minutes 50.79 seconds (12170.79 seconds total)