Starting phenix.real_space_refine on Mon Aug 25 05:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.map" model { file = "/net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n6k_49063/08_2025/9n6k_49063.cif" } resolution = 2.9 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= 0.007 sd= 0.030 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 324 5.49 5 S 60 5.16 5 C 15311 2.51 5 N 4756 2.21 5 O 5507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 25958 Number of models: 1 Model: "" Number of chains: 12 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: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "L" Number of atoms: 6010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6010 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 23, 'TRANS': 743} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 20, 'ASP:plan': 9, 'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "K" Number of atoms: 7191 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 989, 7187 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 957} Chain breaks: 8 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 951 Unresolved non-hydrogen angles: 1189 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'PHE:plan': 10, 'GLU:plan': 37, 'ASP:plan': 19, 'GLN:plan1': 7, 'ARG:plan': 13, 'ASN:plan1': 13, 'TYR:plan': 9, 'HIS:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 502 Conformer: "B" Number of residues, atoms: 989, 7187 Classifications: {'peptide': 989} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 957} Chain breaks: 8 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 951 Unresolved non-hydrogen angles: 1189 Unresolved non-hydrogen dihedrals: 797 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'PHE:plan': 10, 'GLU:plan': 37, 'ASP:plan': 19, 'GLN:plan1': 7, 'ARG:plan': 13, 'ASN:plan1': 13, 'TYR:plan': 9, 'HIS:plan': 3, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 502 bond proxies already assigned to first conformer: 7295 Chain: "I" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3296 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain breaks: 1 Chain: "J" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3348 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain breaks: 1 Time building chain proxies: 6.32, per 1000 atoms: 0.24 Number of scatterers: 25958 At special positions: 0 Unit cell: (142.854, 131.3, 234.239, 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 324 15.00 O 5507 8.00 N 4756 7.00 C 15311 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: 1.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4794 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 19 sheets defined 56.2% alpha, 7.9% beta 154 base pairs and 293 stacking pairs defined. Time for finding SS restraints: 3.60 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: 3.962A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.554A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 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: 4.337A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.579A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 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 removed outlier: 3.504A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.573A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.962A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.555A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.337A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.579A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 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 removed outlier: 3.503A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.573A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.513A 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 132 Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.512A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'L' and resid 203 through 209 removed outlier: 3.912A pdb=" N GLU L 209 " --> pdb=" O ASN L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 234 removed outlier: 3.631A pdb=" N GLY L 234 " --> pdb=" O TYR L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 259 removed outlier: 3.564A pdb=" N LEU L 242 " --> pdb=" O GLY L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 283 Processing helix 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: 3.717A pdb=" N VAL L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN L 343 " --> pdb=" O GLN L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 392 Processing helix chain 'L' and resid 406 through 421 Processing helix chain 'L' and resid 436 through 448 removed outlier: 3.926A pdb=" N THR L 443 " --> pdb=" O ALA L 439 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA L 448 " --> pdb=" O PHE L 444 " (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 498 through 503 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: 3.713A pdb=" N GLU L 527 " --> pdb=" O SER L 523 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER L 531 " --> pdb=" O GLU L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 560 removed outlier: 4.139A pdb=" N LEU L 552 " --> pdb=" O ASN L 548 " (cutoff:3.500A) Processing helix chain 'L' and resid 576 through 590 removed outlier: 3.930A 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: 3.814A pdb=" N VAL L 672 " --> pdb=" O ALA L 668 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS L 675 " --> pdb=" O ARG L 671 " (cutoff:3.500A) Processing helix chain 'L' and resid 684 through 694 removed outlier: 3.743A pdb=" N ARG L 688 " --> pdb=" O GLU L 684 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER L 694 " --> pdb=" O LEU L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 695 through 710 removed outlier: 4.543A pdb=" N LEU L 699 " --> pdb=" O GLY L 695 " (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: 3.656A pdb=" N ASP L 798 " --> pdb=" O ASN L 794 " (cutoff:3.500A) Processing helix chain 'L' and resid 825 through 843 removed outlier: 3.578A 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 931 through 936 removed outlier: 4.003A pdb=" N ILE L 936 " --> pdb=" O TRP L 932 " (cutoff:3.500A) Processing helix chain 'L' and resid 937 through 954 removed outlier: 3.653A pdb=" N LYS L 943 " --> pdb=" O GLU L 939 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 147 removed outlier: 4.561A pdb=" N ASP K 145 " --> pdb=" O SER K 142 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU K 147 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 234 removed outlier: 3.577A pdb=" N GLY K 234 " --> pdb=" O TYR K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 259 Processing helix chain 'K' and resid 263 through 283 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: 3.726A pdb=" N VAL K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) removed outlier: 4.058A 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: 3.953A pdb=" N THR K 443 " --> pdb=" O ALA K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 471 removed outlier: 3.753A pdb=" N PHE K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 491 through 498 Processing helix chain 'K' and resid 498 through 504 removed outlier: 3.962A pdb=" N SER K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 516 through 520 removed outlier: 4.470A pdb=" N ASN K 520 " --> pdb=" O ARG K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 531 Processing helix chain 'K' and resid 548 through 560 removed outlier: 4.034A 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: 3.613A pdb=" N VAL K 672 " --> pdb=" O ALA K 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 683 through 693 removed outlier: 3.572A pdb=" N MET K 692 " --> pdb=" O ARG K 688 " (cutoff:3.500A) Processing helix chain 'K' and resid 696 through 710 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 803 removed outlier: 3.830A pdb=" N ASP K 798 " --> pdb=" O ASN K 794 " (cutoff:3.500A) Processing helix chain 'K' and resid 825 through 844 removed outlier: 3.574A pdb=" N VAL K 829 " --> pdb=" O VAL K 825 " (cutoff:3.500A) Processing helix chain 'K' and resid 845 through 848 removed outlier: 4.110A pdb=" N VAL K 848 " --> pdb=" O SER K 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 845 through 848' Processing helix chain 'K' and resid 857 through 873 removed outlier: 3.749A pdb=" N ALA K 862 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY K 863 " --> pdb=" O GLU K 859 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER K 866 " --> pdb=" O ALA K 862 " (cutoff:3.500A) Processing helix chain 'K' and resid 913 through 917 removed outlier: 3.502A pdb=" N PHE K 917 " --> pdb=" O GLY K 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 913 through 917' Processing helix chain 'K' and resid 937 through 954 removed outlier: 3.808A pdb=" N LYS K 943 " --> pdb=" O GLU K 939 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS K 952 " --> pdb=" O GLU K 948 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP K 953 " --> pdb=" O GLN K 949 " (cutoff:3.500A) Processing helix chain 'K' and resid 1011 through 1025 Processing helix chain 'K' and resid 1031 through 1038 removed outlier: 3.615A pdb=" N ALA K1037 " --> pdb=" O ASP K1033 " (cutoff:3.500A) Processing helix chain 'K' and resid 1045 through 1090 removed outlier: 3.904A pdb=" N LYS K1061 " --> pdb=" O MET K1057 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP K1062 " --> pdb=" O GLU K1058 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K1067 " --> pdb=" O CYS K1063 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN K1070 " --> pdb=" O GLU K1066 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU K1073 " --> pdb=" O LYS K1069 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU K1075 " --> pdb=" O ARG K1071 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU K1076 " --> pdb=" O LYS K1072 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS K1077 " --> pdb=" O GLU K1073 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA K1084 " --> pdb=" O LYS K1080 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA K1087 " --> pdb=" O THR K1083 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS K1088 " --> pdb=" O ALA K1084 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU K1089 " --> pdb=" O TYR K1085 " (cutoff:3.500A) Processing helix chain 'K' and resid 1104 through 1113 Processing helix chain 'K' and resid 1130 through 1151 removed outlier: 3.666A pdb=" N LEU K1134 " --> pdb=" O ALA K1130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN K1150 " --> pdb=" O LEU K1146 " (cutoff:3.500A) Processing helix chain 'K' and resid 1154 through 1158 removed outlier: 3.536A pdb=" N LYS K1157 " --> pdb=" O ASP K1154 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE K1158 " --> pdb=" O PRO K1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1154 through 1158' Processing helix chain 'K' and resid 1176 through 1190 removed outlier: 3.613A pdb=" N PHE K1188 " --> pdb=" O LEU K1184 " (cutoff:3.500A) Processing helix chain 'K' and resid 1194 through 1201 Processing helix chain 'K' and resid 1249 through 1265 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.484A 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: 6.390A 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: 7.156A 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: 7.421A 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: 7.067A 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: 5.329A pdb=" N VAL L 182 " --> pdb=" O LYS L 216 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS L 216 " --> pdb=" O VAL L 182 " (cutoff:3.500A) removed outlier: 4.145A 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: 5.690A pdb=" N ILE L 290 " --> pdb=" O LYS L 310 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS L 310 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 3.989A 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 455 removed outlier: 6.616A pdb=" N ILE L 454 " --> pdb=" O LEU L 489 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN L 508 " --> pdb=" O ASN L 536 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N MET L 538 " --> pdb=" O GLN L 508 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET L 510 " --> pdb=" O MET L 538 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE L 540 " --> pdb=" O MET L 510 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL L 512 " --> pdb=" O ILE L 540 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY L 397 " --> pdb=" O LEU L 539 " (cutoff:3.500A) removed outlier: 6.857A 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: 6.694A pdb=" N GLN L 739 " --> pdb=" O LEU L 768 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N SER L 770 " --> pdb=" O GLN L 739 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU L 741 " --> pdb=" O SER L 770 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL L 714 " --> pdb=" O PHE L 767 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU L 769 " --> pdb=" O VAL L 714 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE L 716 " --> pdb=" O LEU L 769 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL L 786 " --> pdb=" O TYR L 817 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU L 819 " --> pdb=" O VAL L 786 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE L 788 " --> pdb=" O LEU L 819 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N SER L 821 " --> pdb=" O ILE L 788 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR L 610 " --> pdb=" O VAL L 816 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ARG L 818 " --> pdb=" O THR L 610 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG L 612 " --> pdb=" O ARG L 818 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL L 820 " --> pdb=" O ARG L 612 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU L 614 " --> pdb=" O VAL L 820 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR L 924 " --> pdb=" O GLU L 611 " (cutoff:3.500A) removed outlier: 6.424A 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: 5.328A pdb=" N VAL K 182 " --> pdb=" O LYS K 216 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS K 216 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 4.092A 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: 6.496A pdb=" N LEU K 308 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER K 293 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN K 306 " --> pdb=" O SER K 293 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG K 295 " --> pdb=" O GLN K 304 " (cutoff:3.500A) removed outlier: 5.891A 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: 6.519A pdb=" N ILE K 454 " --> pdb=" O LEU K 489 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN K 508 " --> pdb=" O ASN K 536 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N MET K 538 " --> pdb=" O GLN K 508 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET K 510 " --> pdb=" O MET K 538 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE K 540 " --> pdb=" O MET K 510 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL K 512 " --> pdb=" O ILE K 540 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY K 397 " --> pdb=" O LEU K 539 " (cutoff:3.500A) removed outlier: 6.718A 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: 6.745A pdb=" N GLN K 739 " --> pdb=" O LEU K 768 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N SER K 770 " --> pdb=" O GLN K 739 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU K 741 " --> pdb=" O SER K 770 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL K 714 " --> pdb=" O PHE K 767 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU K 769 " --> pdb=" O VAL K 714 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE K 716 " --> pdb=" O LEU K 769 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR K 924 " --> pdb=" O GLU K 611 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE K 613 " --> pdb=" O THR K 924 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR K 926 " --> pdb=" O ILE K 613 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG K 615 " --> pdb=" O TYR K 926 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 1119 through 1120 995 hydrogen bonds defined for protein. 2905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 397 hydrogen bonds 778 hydrogen bond angles 0 basepair planarities 154 basepair parallelities 293 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4073 1.32 - 1.45: 8463 1.45 - 1.57: 13788 1.57 - 1.69: 644 1.69 - 1.82: 108 Bond restraints: 27076 Sorted by residual: bond pdb=" CA ALA A 127 " pdb=" CB ALA A 127 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.55e-02 4.16e+03 9.45e+00 bond pdb=" N ILE L 930 " pdb=" CA ILE L 930 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.30e-02 5.92e+03 9.34e+00 bond pdb=" C ARG E 128 " pdb=" O ARG E 128 " ideal model delta sigma weight residual 1.237 1.201 0.035 1.17e-02 7.31e+03 9.18e+00 bond pdb=" CA ALA H 114 " pdb=" CB ALA H 114 " ideal model delta sigma weight residual 1.529 1.483 0.046 1.55e-02 4.16e+03 8.70e+00 bond pdb=" CA ALA E 127 " pdb=" CB ALA E 127 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.58e-02 4.01e+03 8.12e+00 ... (remaining 27071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 37164 2.13 - 4.26: 779 4.26 - 6.39: 65 6.39 - 8.51: 27 8.51 - 10.64: 2 Bond angle restraints: 38037 Sorted by residual: angle pdb=" N VAL H 115 " pdb=" CA VAL H 115 " pdb=" C VAL H 115 " ideal model delta sigma weight residual 110.62 105.04 5.58 1.02e+00 9.61e-01 2.99e+01 angle pdb=" C ILE L 251 " pdb=" N GLU L 252 " pdb=" CA GLU L 252 " ideal model delta sigma weight residual 121.58 110.94 10.64 1.95e+00 2.63e-01 2.98e+01 angle pdb=" C LYS K 822 " pdb=" N ASP K 823 " pdb=" CA ASP K 823 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.44e+01 angle pdb=" O GLY H 111 " pdb=" C GLY H 111 " pdb=" N THR H 112 " ideal model delta sigma weight residual 122.70 116.81 5.89 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N SER H 120 " pdb=" CA SER H 120 " pdb=" C SER H 120 " ideal model delta sigma weight residual 111.07 106.53 4.54 1.07e+00 8.73e-01 1.80e+01 ... (remaining 38032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.59: 13377 29.59 - 59.18: 1962 59.18 - 88.78: 76 88.78 - 118.37: 0 118.37 - 147.96: 2 Dihedral angle restraints: 15417 sinusoidal: 8029 harmonic: 7388 Sorted by residual: dihedral pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " pdb=" CZ ARG E 129 " pdb=" NH1 ARG E 129 " ideal model delta sinusoidal sigma weight residual 0.00 -72.12 72.12 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 -60.63 60.63 1 1.00e+01 1.00e-02 4.89e+01 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 -147.24 -32.76 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 15414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3476 0.051 - 0.103: 655 0.103 - 0.154: 163 0.154 - 0.206: 21 0.206 - 0.257: 6 Chirality restraints: 4321 Sorted by residual: chirality pdb=" CB ILE L 429 " pdb=" CA ILE L 429 " pdb=" CG1 ILE L 429 " pdb=" CG2 ILE L 429 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+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 1.37e+00 chirality pdb=" CA ASP K 823 " pdb=" N ASP K 823 " pdb=" C ASP K 823 " pdb=" CB ASP K 823 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4318 not shown) Planarity restraints: 3781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 129 " -1.033 9.50e-02 1.11e+02 4.63e-01 1.29e+02 pdb=" NE ARG E 129 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 129 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 129 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 129 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.956 9.50e-02 1.11e+02 4.29e-01 1.11e+02 pdb=" NE ARG A 129 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 128 " -0.806 9.50e-02 1.11e+02 3.61e-01 7.94e+01 pdb=" NE ARG E 128 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG E 128 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 128 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 128 " -0.024 2.00e-02 2.50e+03 ... (remaining 3778 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 788 2.70 - 3.25: 22229 3.25 - 3.80: 45977 3.80 - 4.35: 58542 4.35 - 4.90: 87982 Nonbonded interactions: 215518 Sorted by model distance: nonbonded pdb=" NE2 GLN L 410 " pdb=" NH2 ARG L 597 " model vdw 2.145 3.200 nonbonded pdb=" O LYS L 627 " pdb=" OG1 THR L 631 " model vdw 2.284 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.289 2.496 nonbonded pdb=" OD2 ASP E 81 " pdb=" OH TYR L 634 " model vdw 2.304 3.040 nonbonded pdb=" O2 DC I -33 " pdb=" N2 DG J 33 " model vdw 2.307 2.496 ... (remaining 215513 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' selection = chain 'E' } 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 118)) selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e 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' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.320 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 0.053 27076 Z= 0.210 Angle : 0.718 10.642 38037 Z= 0.424 Chirality : 0.046 0.257 4321 Planarity : 0.013 0.463 3781 Dihedral : 22.218 147.962 10623 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.05 % Allowed : 1.60 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -2.10 (0.14), residues: 2489 helix: -1.41 (0.12), residues: 1327 sheet: 0.18 (0.39), residues: 180 loop : -1.46 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 29 TYR 0.028 0.002 TYR D 80 PHE 0.026 0.002 PHE L 767 TRP 0.013 0.001 TRP K 311 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00389 (27076) covalent geometry : angle 0.71828 (38037) hydrogen bonds : bond 0.15096 ( 1392) hydrogen bonds : angle 5.71802 ( 3683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 351 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 ASP cc_start: 0.8827 (m-30) cc_final: 0.8600 (m-30) REVERT: C 90 ASP cc_start: 0.8568 (t70) cc_final: 0.8326 (t0) REVERT: C 104 GLN cc_start: 0.8412 (mm110) cc_final: 0.8194 (mt0) REVERT: D 30 ARG cc_start: 0.7336 (ttm170) cc_final: 0.6931 (mmp80) REVERT: D 65 ASP cc_start: 0.8865 (t0) cc_final: 0.8629 (t0) REVERT: D 68 GLU cc_start: 0.8375 (tp30) cc_final: 0.7968 (mm-30) REVERT: D 110 GLU cc_start: 0.8654 (tp30) cc_final: 0.8379 (tp30) REVERT: G 72 ASP cc_start: 0.8557 (m-30) cc_final: 0.8337 (m-30) REVERT: L 318 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7463 (tm-30) REVERT: L 528 SER cc_start: 0.8374 (m) cc_final: 0.8105 (p) REVERT: L 673 LEU cc_start: 0.7965 (mm) cc_final: 0.7121 (pp) REVERT: K 318 GLU cc_start: 0.8398 (mp0) cc_final: 0.8096 (mp0) REVERT: K 353 ASN cc_start: 0.8738 (t0) cc_final: 0.8486 (t0) REVERT: K 802 MET cc_start: 0.8652 (ptp) cc_final: 0.8296 (ptp) outliers start: 1 outliers final: 1 residues processed: 352 average time/residue: 0.7687 time to fit residues: 302.5393 Evaluate side-chains 190 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 252 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN F 25 ASN F 93 GLN G 73 ASN G 110 ASN E 85 GLN A 68 GLN A 85 GLN L 428 HIS L 516 HIS L 591 GLN L 667 ASN L 813 HIS K 132 ASN K 185 HIS K 222 HIS K 508 GLN K 591 GLN ** K 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076049 restraints weight = 62275.161| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.20 r_work: 0.3054 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 27076 Z= 0.327 Angle : 0.650 8.702 38037 Z= 0.363 Chirality : 0.043 0.169 4321 Planarity : 0.004 0.050 3781 Dihedral : 25.621 158.075 6281 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.45 % Allowed : 12.03 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.31 (0.16), residues: 2489 helix: 0.48 (0.14), residues: 1338 sheet: 0.39 (0.38), residues: 183 loop : -1.23 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 476 TYR 0.021 0.002 TYR G 50 PHE 0.020 0.002 PHE K 917 TRP 0.012 0.001 TRP K 217 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00734 (27076) covalent geometry : angle 0.64964 (38037) hydrogen bonds : bond 0.05618 ( 1392) hydrogen bonds : angle 3.76395 ( 3683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8620 (mt-10) REVERT: C 104 GLN cc_start: 0.8549 (mm110) cc_final: 0.8254 (mm-40) REVERT: D 110 GLU cc_start: 0.8761 (tp30) cc_final: 0.8547 (tp30) REVERT: H 73 GLU cc_start: 0.8741 (tp30) cc_final: 0.8514 (tm-30) REVERT: E 94 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8346 (mt-10) REVERT: E 133 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: A 64 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9040 (mppt) REVERT: L 528 SER cc_start: 0.9110 (m) cc_final: 0.8812 (t) REVERT: L 538 MET cc_start: 0.8036 (ttt) cc_final: 0.7824 (ttt) REVERT: K 692 MET cc_start: 0.8802 (mpp) cc_final: 0.8500 (mpp) REVERT: K 781 MET cc_start: 0.7968 (mtp) cc_final: 0.7727 (mtp) REVERT: K 802 MET cc_start: 0.8796 (ptp) cc_final: 0.8458 (ptp) outliers start: 46 outliers final: 12 residues processed: 226 average time/residue: 0.7983 time to fit residues: 203.1507 Evaluate side-chains 173 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 469 TYR Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 825 VAL Chi-restraints excluded: chain K residue 816 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 167 optimal weight: 4.9990 chunk 228 optimal weight: 0.0770 chunk 242 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN L 385 ASN L 667 ASN K 132 ASN K 546 GLN K 653 ASN K 660 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.118868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.078974 restraints weight = 62512.648| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.21 r_work: 0.3128 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27076 Z= 0.137 Angle : 0.540 9.289 38037 Z= 0.305 Chirality : 0.037 0.173 4321 Planarity : 0.003 0.043 3781 Dihedral : 25.272 150.847 6278 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.81 % Allowed : 14.69 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.44 (0.16), residues: 2489 helix: 1.25 (0.14), residues: 1340 sheet: 0.42 (0.40), residues: 171 loop : -1.06 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 276 TYR 0.018 0.001 TYR L 841 PHE 0.026 0.001 PHE L 738 TRP 0.011 0.001 TRP L 311 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00298 (27076) covalent geometry : angle 0.54023 (38037) hydrogen bonds : bond 0.04229 ( 1392) hydrogen bonds : angle 3.41033 ( 3683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6373 (mtpp) REVERT: C 92 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8559 (mt-10) REVERT: C 99 ARG cc_start: 0.8630 (mmp-170) cc_final: 0.8342 (mmm-85) REVERT: C 104 GLN cc_start: 0.8475 (mm110) cc_final: 0.8155 (mm110) REVERT: G 15 LYS cc_start: 0.8519 (ttpm) cc_final: 0.8301 (ttpp) REVERT: E 94 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8183 (mt-10) REVERT: E 120 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: A 129 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8492 (tmm160) REVERT: L 483 MET cc_start: 0.8500 (mmt) cc_final: 0.8131 (mmp) REVERT: L 528 SER cc_start: 0.9114 (m) cc_final: 0.8778 (t) REVERT: L 700 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8680 (tm) REVERT: L 781 MET cc_start: 0.8086 (mmp) cc_final: 0.7850 (mmm) REVERT: L 785 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7402 (p) REVERT: K 276 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8542 (ttp80) REVERT: K 353 ASN cc_start: 0.8661 (t0) cc_final: 0.8370 (t0) REVERT: K 437 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7441 (tmm) REVERT: K 692 MET cc_start: 0.8819 (mpp) cc_final: 0.8562 (mpp) REVERT: K 781 MET cc_start: 0.7860 (mtp) cc_final: 0.7611 (mtp) REVERT: K 800 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: K 802 MET cc_start: 0.8811 (ptp) cc_final: 0.8480 (ptp) outliers start: 34 outliers final: 7 residues processed: 197 average time/residue: 0.8219 time to fit residues: 183.0238 Evaluate side-chains 175 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain L residue 246 CYS Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 563 ARG Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain K residue 800 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 11 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN L 633 ASN K 132 ASN K 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.117294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076938 restraints weight = 61888.547| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.14 r_work: 0.3084 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 27076 Z= 0.183 Angle : 0.549 9.621 38037 Z= 0.309 Chirality : 0.038 0.154 4321 Planarity : 0.003 0.039 3781 Dihedral : 25.333 155.796 6278 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.92 % Allowed : 15.54 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.75 (0.17), residues: 2489 helix: 1.50 (0.14), residues: 1355 sheet: 0.52 (0.39), residues: 177 loop : -0.96 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 276 TYR 0.013 0.001 TYR L 841 PHE 0.022 0.001 PHE L 738 TRP 0.010 0.001 TRP L 311 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00408 (27076) covalent geometry : angle 0.54927 (38037) hydrogen bonds : bond 0.04386 ( 1392) hydrogen bonds : angle 3.30548 ( 3683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: C 104 GLN cc_start: 0.8513 (mm110) cc_final: 0.8176 (mm110) REVERT: H 102 GLU cc_start: 0.8638 (tt0) cc_final: 0.8396 (tt0) REVERT: E 94 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8251 (mt-10) REVERT: E 120 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8345 (mtm) REVERT: A 59 GLU cc_start: 0.8334 (pm20) cc_final: 0.8035 (pm20) REVERT: A 129 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8458 (tmm160) REVERT: L 528 SER cc_start: 0.9032 (m) cc_final: 0.8740 (t) REVERT: L 700 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8841 (tm) REVERT: L 785 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7581 (p) REVERT: L 802 MET cc_start: 0.8609 (pmm) cc_final: 0.8400 (pmm) REVERT: K 270 MET cc_start: 0.7890 (ppp) cc_final: 0.7688 (pp-130) REVERT: K 276 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8416 (ttp80) REVERT: K 437 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7593 (tmm) REVERT: K 692 MET cc_start: 0.8798 (mpp) cc_final: 0.8584 (mpp) REVERT: K 781 MET cc_start: 0.8153 (mtp) cc_final: 0.7872 (mtp) REVERT: K 800 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: K 802 MET cc_start: 0.8883 (ptp) cc_final: 0.8567 (ptp) outliers start: 36 outliers final: 10 residues processed: 188 average time/residue: 0.8881 time to fit residues: 190.1205 Evaluate side-chains 171 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain L residue 453 CYS Chi-restraints excluded: chain L residue 652 MET Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 381 LEU Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain K residue 800 GLN Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 116 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN K 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.117230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.077006 restraints weight = 61877.433| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.16 r_work: 0.3088 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 27076 Z= 0.168 Angle : 0.536 9.990 38037 Z= 0.302 Chirality : 0.038 0.161 4321 Planarity : 0.003 0.038 3781 Dihedral : 25.286 153.362 6278 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.92 % Allowed : 15.86 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.93 (0.17), residues: 2489 helix: 1.68 (0.14), residues: 1354 sheet: 0.44 (0.40), residues: 178 loop : -0.91 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 20 TYR 0.013 0.001 TYR K 494 PHE 0.019 0.001 PHE L 738 TRP 0.010 0.001 TRP L 311 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00374 (27076) covalent geometry : angle 0.53646 (38037) hydrogen bonds : bond 0.04181 ( 1392) hydrogen bonds : angle 3.24324 ( 3683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.916 Fit side-chains REVERT: B 16 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7441 (mmtm) REVERT: C 104 GLN cc_start: 0.8493 (mm110) cc_final: 0.8142 (mm110) REVERT: E 59 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: E 120 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: E 133 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 59 GLU cc_start: 0.8317 (pm20) cc_final: 0.8053 (pm20) REVERT: L 389 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 444 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8218 (t80) REVERT: L 700 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8819 (tm) REVERT: L 781 MET cc_start: 0.8432 (mmp) cc_final: 0.8212 (mmm) REVERT: L 785 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7706 (p) REVERT: L 802 MET cc_start: 0.8610 (pmm) cc_final: 0.7418 (pmm) REVERT: K 270 MET cc_start: 0.8042 (ppp) cc_final: 0.7804 (pp-130) REVERT: K 276 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8538 (ttp80) REVERT: K 437 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7623 (tmm) REVERT: K 781 MET cc_start: 0.8138 (mtp) cc_final: 0.7772 (mtp) REVERT: K 800 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: K 802 MET cc_start: 0.8891 (ptp) cc_final: 0.8651 (ptp) REVERT: K 919 LYS cc_start: 0.7785 (tptp) cc_final: 0.7354 (mmtm) REVERT: K 920 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6690 (pm20) outliers start: 36 outliers final: 7 residues processed: 186 average time/residue: 0.9004 time to fit residues: 189.6553 Evaluate side-chains 170 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 444 PHE Chi-restraints excluded: chain L residue 457 MET Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 437 MET Chi-restraints excluded: chain K residue 800 GLN Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 161 optimal weight: 10.0000 chunk 145 optimal weight: 0.0170 chunk 77 optimal weight: 20.0000 chunk 129 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN L 806 HIS K 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.116259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075865 restraints weight = 61914.374| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.18 r_work: 0.3058 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 27076 Z= 0.203 Angle : 0.552 9.800 38037 Z= 0.310 Chirality : 0.039 0.156 4321 Planarity : 0.003 0.036 3781 Dihedral : 25.400 157.287 6278 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.86 % Allowed : 16.07 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 0.92 (0.17), residues: 2489 helix: 1.70 (0.14), residues: 1356 sheet: 0.21 (0.39), residues: 190 loop : -0.91 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 476 TYR 0.013 0.001 TYR K 494 PHE 0.021 0.001 PHE K 917 TRP 0.010 0.001 TRP K 311 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00454 (27076) covalent geometry : angle 0.55235 (38037) hydrogen bonds : bond 0.04461 ( 1392) hydrogen bonds : angle 3.26503 ( 3683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.951 Fit side-chains REVERT: B 16 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7564 (mmtm) REVERT: C 104 GLN cc_start: 0.8503 (mm110) cc_final: 0.8159 (mm110) REVERT: D 102 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: G 99 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8184 (mtp180) REVERT: H 73 GLU cc_start: 0.8706 (tp30) cc_final: 0.8407 (tm-30) REVERT: E 59 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: E 120 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: E 133 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: A 59 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: A 129 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8450 (tmm160) REVERT: L 389 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: L 444 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8167 (t80) REVERT: L 692 MET cc_start: 0.8424 (mmm) cc_final: 0.7839 (mmp) REVERT: L 700 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9006 (tm) REVERT: L 785 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.7880 (p) REVERT: K 270 MET cc_start: 0.8152 (ppp) cc_final: 0.7919 (pp-130) REVERT: K 276 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8492 (ttp80) REVERT: K 781 MET cc_start: 0.8267 (mtp) cc_final: 0.7969 (mtp) REVERT: K 800 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: K 802 MET cc_start: 0.8940 (ptp) cc_final: 0.8652 (ptp) REVERT: K 831 GLU cc_start: 0.8335 (tp30) cc_final: 0.8081 (pp20) REVERT: K 919 LYS cc_start: 0.7846 (tptp) cc_final: 0.7396 (mptp) REVERT: K 920 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6779 (pm20) outliers start: 35 outliers final: 7 residues processed: 183 average time/residue: 0.8853 time to fit residues: 182.3118 Evaluate side-chains 174 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 444 PHE Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 800 GLN Chi-restraints excluded: chain K residue 816 VAL Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 62 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 209 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN A 68 GLN L 339 GLN L 806 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.117181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077074 restraints weight = 61908.083| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.20 r_work: 0.3089 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27076 Z= 0.134 Angle : 0.534 10.384 38037 Z= 0.301 Chirality : 0.037 0.164 4321 Planarity : 0.003 0.040 3781 Dihedral : 25.392 156.247 6278 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.70 % Allowed : 16.60 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.07 (0.17), residues: 2489 helix: 1.80 (0.14), residues: 1357 sheet: 0.44 (0.40), residues: 179 loop : -0.85 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 476 TYR 0.012 0.001 TYR K 494 PHE 0.017 0.001 PHE K 338 TRP 0.012 0.001 TRP L 311 HIS 0.004 0.001 HIS L 806 Details of bonding type rmsd covalent geometry : bond 0.00291 (27076) covalent geometry : angle 0.53442 (38037) hydrogen bonds : bond 0.04114 ( 1392) hydrogen bonds : angle 3.22838 ( 3683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.909 Fit side-chains REVERT: B 16 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7552 (mmtm) REVERT: C 104 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8183 (mm110) REVERT: G 99 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8158 (mtp180) REVERT: H 73 GLU cc_start: 0.8689 (tp30) cc_final: 0.8365 (tm-30) REVERT: E 59 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: E 120 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8299 (mtm) REVERT: E 133 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: A 59 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: A 129 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8435 (tmm160) REVERT: L 389 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: L 444 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8156 (t80) REVERT: L 692 MET cc_start: 0.8384 (mmm) cc_final: 0.7802 (mmp) REVERT: L 700 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8886 (tm) REVERT: L 785 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7972 (p) REVERT: K 270 MET cc_start: 0.8149 (ppp) cc_final: 0.7909 (pp-130) REVERT: K 276 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8472 (ttp80) REVERT: K 781 MET cc_start: 0.8217 (mtp) cc_final: 0.7959 (mtp) REVERT: K 800 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: K 802 MET cc_start: 0.8931 (ptp) cc_final: 0.8674 (ptp) REVERT: K 831 GLU cc_start: 0.8290 (tp30) cc_final: 0.7883 (tm-30) REVERT: K 919 LYS cc_start: 0.7859 (tptp) cc_final: 0.7430 (mptp) REVERT: K 920 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6715 (pm20) outliers start: 32 outliers final: 5 residues processed: 180 average time/residue: 0.8883 time to fit residues: 179.7983 Evaluate side-chains 174 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 444 PHE Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 800 GLN Chi-restraints excluded: chain K residue 816 VAL Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 240 optimal weight: 40.0000 chunk 135 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN L 806 HIS K 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.115586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075194 restraints weight = 61558.717| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.17 r_work: 0.3043 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 27076 Z= 0.220 Angle : 0.568 10.171 38037 Z= 0.318 Chirality : 0.039 0.163 4321 Planarity : 0.003 0.036 3781 Dihedral : 25.468 158.753 6278 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.92 % Allowed : 16.55 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.00 (0.17), residues: 2489 helix: 1.75 (0.14), residues: 1357 sheet: 0.08 (0.37), residues: 204 loop : -0.84 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 476 TYR 0.013 0.001 TYR K 494 PHE 0.016 0.001 PHE K 338 TRP 0.010 0.001 TRP K 311 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00494 (27076) covalent geometry : angle 0.56838 (38037) hydrogen bonds : bond 0.04648 ( 1392) hydrogen bonds : angle 3.30318 ( 3683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.911 Fit side-chains REVERT: B 16 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7660 (mmtm) REVERT: C 92 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: C 104 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8210 (mm110) REVERT: D 32 GLU cc_start: 0.7886 (tp30) cc_final: 0.7606 (tp30) REVERT: G 99 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8132 (mtp180) REVERT: H 73 GLU cc_start: 0.8687 (tp30) cc_final: 0.8385 (tm-30) REVERT: E 120 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8430 (mtm) REVERT: E 133 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 59 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 129 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8418 (tmm160) REVERT: L 692 MET cc_start: 0.8623 (mmm) cc_final: 0.8115 (mmp) REVERT: L 700 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9072 (tm) REVERT: L 785 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7802 (p) REVERT: L 802 MET cc_start: 0.8692 (pmm) cc_final: 0.8350 (pmm) REVERT: K 276 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8479 (ttp80) REVERT: K 781 MET cc_start: 0.8296 (mtp) cc_final: 0.8077 (mtp) REVERT: K 802 MET cc_start: 0.8928 (ptp) cc_final: 0.8654 (ptp) REVERT: K 831 GLU cc_start: 0.8380 (tp30) cc_final: 0.8089 (pp20) REVERT: K 919 LYS cc_start: 0.7840 (tptp) cc_final: 0.7439 (mptp) REVERT: K 920 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: K 926 TYR cc_start: 0.7780 (t80) cc_final: 0.7520 (t80) outliers start: 36 outliers final: 8 residues processed: 187 average time/residue: 0.8895 time to fit residues: 188.5673 Evaluate side-chains 168 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 816 VAL Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 5 optimal weight: 2.9990 chunk 222 optimal weight: 0.0470 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 209 optimal weight: 0.0870 chunk 64 optimal weight: 0.0570 chunk 216 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN ** L 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 806 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.116929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.076951 restraints weight = 61710.744| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.16 r_work: 0.3086 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27076 Z= 0.131 Angle : 0.563 12.443 38037 Z= 0.312 Chirality : 0.037 0.170 4321 Planarity : 0.003 0.037 3781 Dihedral : 25.478 157.931 6278 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 17.24 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.11 (0.17), residues: 2489 helix: 1.83 (0.14), residues: 1357 sheet: 0.30 (0.39), residues: 194 loop : -0.80 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 377 TYR 0.015 0.001 TYR K 469 PHE 0.034 0.001 PHE K 917 TRP 0.012 0.001 TRP L 311 HIS 0.004 0.001 HIS K 645 Details of bonding type rmsd covalent geometry : bond 0.00281 (27076) covalent geometry : angle 0.56280 (38037) hydrogen bonds : bond 0.04159 ( 1392) hydrogen bonds : angle 3.27454 ( 3683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.922 Fit side-chains REVERT: B 16 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7648 (mmtm) REVERT: B 79 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8623 (mptp) REVERT: C 92 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: C 104 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8148 (mm110) REVERT: D 32 GLU cc_start: 0.7762 (tp30) cc_final: 0.7554 (tp30) REVERT: G 99 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8112 (mtp180) REVERT: H 73 GLU cc_start: 0.8661 (tp30) cc_final: 0.8342 (tm-30) REVERT: E 120 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: E 133 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: A 59 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: A 129 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8464 (tmm160) REVERT: L 444 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8076 (t80) REVERT: L 692 MET cc_start: 0.8607 (mmm) cc_final: 0.8063 (mmp) REVERT: L 700 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8981 (tm) REVERT: L 785 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.7834 (p) REVERT: L 802 MET cc_start: 0.8710 (pmm) cc_final: 0.8430 (pmm) REVERT: K 270 MET cc_start: 0.7953 (ppp) cc_final: 0.7726 (pp-130) REVERT: K 276 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8458 (ttp80) REVERT: K 802 MET cc_start: 0.8904 (ptp) cc_final: 0.8655 (ptp) REVERT: K 831 GLU cc_start: 0.8357 (tp30) cc_final: 0.7924 (tm-30) REVERT: K 919 LYS cc_start: 0.7833 (tptp) cc_final: 0.7427 (mmtm) REVERT: K 920 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: K 926 TYR cc_start: 0.7755 (t80) cc_final: 0.7493 (t80) outliers start: 32 outliers final: 7 residues processed: 181 average time/residue: 0.9059 time to fit residues: 185.2410 Evaluate side-chains 171 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 444 PHE Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 785 THR Chi-restraints excluded: chain L residue 868 ILE Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 816 VAL Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 276 optimal weight: 10.0000 chunk 215 optimal weight: 0.0980 chunk 140 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN L 653 ASN L 806 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.116963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077053 restraints weight = 62087.164| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.17 r_work: 0.3094 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27076 Z= 0.149 Angle : 0.553 11.758 38037 Z= 0.307 Chirality : 0.037 0.170 4321 Planarity : 0.003 0.038 3781 Dihedral : 25.270 156.906 6278 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.28 % Allowed : 17.94 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.19 (0.17), residues: 2489 helix: 1.90 (0.14), residues: 1362 sheet: 0.30 (0.39), residues: 195 loop : -0.76 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 476 TYR 0.012 0.001 TYR K 261 PHE 0.017 0.001 PHE L 414 TRP 0.012 0.001 TRP L 311 HIS 0.003 0.001 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00331 (27076) covalent geometry : angle 0.55306 (38037) hydrogen bonds : bond 0.04063 ( 1392) hydrogen bonds : angle 3.23982 ( 3683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4978 Ramachandran restraints generated. 2489 Oldfield, 0 Emsley, 2489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.921 Fit side-chains REVERT: C 92 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: D 32 GLU cc_start: 0.7765 (tp30) cc_final: 0.7555 (tp30) REVERT: D 56 MET cc_start: 0.9081 (mmm) cc_final: 0.8881 (mmm) REVERT: D 102 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: G 99 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8163 (mtp180) REVERT: E 120 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: E 133 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 59 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: A 129 ARG cc_start: 0.8735 (mmm160) cc_final: 0.8525 (tmm160) REVERT: L 444 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8109 (t80) REVERT: L 692 MET cc_start: 0.8588 (mmm) cc_final: 0.8030 (mmp) REVERT: L 700 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9083 (tm) REVERT: L 802 MET cc_start: 0.8709 (pmm) cc_final: 0.8449 (pmm) REVERT: L 876 MET cc_start: 0.4663 (mpp) cc_final: 0.3960 (pmm) REVERT: K 270 MET cc_start: 0.7952 (ppp) cc_final: 0.7713 (pp-130) REVERT: K 276 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8456 (ttp80) REVERT: K 381 LEU cc_start: 0.9250 (mp) cc_final: 0.8932 (tp) REVERT: K 483 MET cc_start: 0.8835 (mmp) cc_final: 0.8545 (mmp) REVERT: K 720 MET cc_start: 0.8619 (mtt) cc_final: 0.8373 (mtm) REVERT: K 723 MET cc_start: 0.8917 (tpt) cc_final: 0.8416 (tpt) REVERT: K 802 MET cc_start: 0.8949 (ptp) cc_final: 0.8711 (ptp) REVERT: K 831 GLU cc_start: 0.8308 (tp30) cc_final: 0.7885 (tm-30) REVERT: K 919 LYS cc_start: 0.7801 (tptp) cc_final: 0.7445 (mmtm) REVERT: K 920 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6942 (pm20) outliers start: 24 outliers final: 9 residues processed: 176 average time/residue: 0.9426 time to fit residues: 187.2069 Evaluate side-chains 171 residues out of total 2225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain L residue 389 PHE Chi-restraints excluded: chain L residue 444 PHE Chi-restraints excluded: chain L residue 700 LEU Chi-restraints excluded: chain L residue 715 LEU Chi-restraints excluded: chain L residue 868 ILE Chi-restraints excluded: chain K residue 766 VAL Chi-restraints excluded: chain K residue 816 VAL Chi-restraints excluded: chain K residue 920 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 139 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 233 optimal weight: 50.0000 chunk 84 optimal weight: 0.0040 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 68 GLN L 486 ASN L 653 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.116810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076923 restraints weight = 61739.597| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.16 r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27076 Z= 0.155 Angle : 0.555 11.827 38037 Z= 0.308 Chirality : 0.038 0.169 4321 Planarity : 0.003 0.037 3781 Dihedral : 25.264 158.982 6278 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.28 % Allowed : 17.99 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: 1.24 (0.17), residues: 2489 helix: 1.94 (0.14), residues: 1361 sheet: 0.35 (0.39), residues: 195 loop : -0.75 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 476 TYR 0.011 0.001 TYR K 494 PHE 0.027 0.001 PHE L 414 TRP 0.011 0.001 TRP L 311 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00344 (27076) covalent geometry : angle 0.55516 (38037) hydrogen bonds : bond 0.04069 ( 1392) hydrogen bonds : angle 3.21370 ( 3683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13373.20 seconds wall clock time: 227 minutes 38.20 seconds (13658.20 seconds total)