Starting phenix.real_space_refine on Mon Jun 23 12:09:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd6_37126/06_2025/8kd6_37126.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 563 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 92 5.16 5 C 16098 2.51 5 N 4797 2.21 5 O 5666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26982 Number of models: 1 Model: "" Number of chains: 17 Chain: "D" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1875 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1627 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 2 Chain: "O" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3384 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "Y" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3340 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "A" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3073 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 1 Chain: "B" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4505 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 12, 'TRANS': 524} Chain breaks: 2 Chain: "E" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2475 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 718 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.14, per 1000 atoms: 0.60 Number of scatterers: 26982 At special positions: 0 Unit cell: (138.45, 158.33, 176.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 92 16.00 P 328 15.00 O 5666 8.00 N 4797 7.00 C 16098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 58.6% alpha, 3.3% beta 140 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 12.98 Creating SS restraints... Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.611A pdb=" N TRP D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 89 " --> pdb=" O SER D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.718A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 292 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 327 through 337 removed outlier: 4.042A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.636A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'F' and resid 98 through 112 removed outlier: 3.911A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 3.715A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 262 removed outlier: 4.114A pdb=" N TYR F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 290 removed outlier: 4.371A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 330 through 338 Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.545A pdb=" N SER F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 369 removed outlier: 3.994A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS F 369 " --> pdb=" O TRP F 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.556A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 removed outlier: 3.564A pdb=" N GLU O 94 " --> pdb=" O MET O 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 110 " --> pdb=" O ASP O 106 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.959A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.689A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 removed outlier: 3.592A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.367A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.554A pdb=" N TYR R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.550A pdb=" N ARG R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.979A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.524A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 77 removed outlier: 3.525A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE S 124 " --> pdb=" O MET S 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 24 through 29 removed outlier: 3.719A pdb=" N GLN T 27 " --> pdb=" O ASP T 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE T 29 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 3.627A pdb=" N GLY T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 removed outlier: 3.556A pdb=" N ARG U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 removed outlier: 3.608A pdb=" N VAL U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.077A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.520A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 removed outlier: 3.865A pdb=" N LYS U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.520A pdb=" N VAL V 45 " --> pdb=" O VAL V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.575A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.218A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.318A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.567A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.735A pdb=" N ASN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 94 " --> pdb=" O PRO A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 94' Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.568A pdb=" N VAL A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 3.635A pdb=" N TYR A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.991A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 4.012A pdb=" N GLU A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.007A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'B' and resid 664 through 666 No H-bonds generated for 'chain 'B' and resid 664 through 666' Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.649A pdb=" N PHE B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.874A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 838 Processing helix chain 'B' and resid 839 through 841 No H-bonds generated for 'chain 'B' and resid 839 through 841' Processing helix chain 'B' and resid 842 through 848 removed outlier: 3.968A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 3.925A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.046A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 942 removed outlier: 4.768A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 Processing helix chain 'B' and resid 982 through 996 removed outlier: 3.979A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.701A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 4.049A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 4.047A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B1174 " --> pdb=" O LYS B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1185 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1221 through 1232 removed outlier: 3.516A pdb=" N TYR B1232 " --> pdb=" O LEU B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 4.227A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1236 through 1240' Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.583A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 removed outlier: 3.534A pdb=" N MET B1294 " --> pdb=" O VAL B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1307 through 1310 removed outlier: 3.690A pdb=" N LEU B1310 " --> pdb=" O LYS B1307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1307 through 1310' Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.629A pdb=" N ILE E 54 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.748A pdb=" N LEU E 296 " --> pdb=" O PRO E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 310 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.221A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 3.656A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 361' Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 558 Processing helix chain 'G' and resid 305 through 312 Processing helix chain 'G' and resid 321 through 325 removed outlier: 3.586A pdb=" N SER G 324 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 325' Processing helix chain 'G' and resid 337 through 342 removed outlier: 4.191A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN G 342 " --> pdb=" O LYS G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 342' Processing helix chain 'G' and resid 541 through 569 Processing sheet with id=AA1, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AA2, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.644A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.137A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.454A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.942A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'U' and resid 42 through 43 removed outlier: 6.912A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'U' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 236 removed outlier: 8.232A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 270 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 62 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 64 " --> pdb=" O TYR A 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1136 through 1140 Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AB4, first strand: chain 'E' and resid 365 through 366 removed outlier: 3.708A pdb=" N SER E 373 " --> pdb=" O LYS E 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AB6, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.350A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.809A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 963 hydrogen bonds defined for protein. 2826 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 15.70 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7513 1.34 - 1.46: 8211 1.46 - 1.58: 11674 1.58 - 1.71: 655 1.71 - 1.83: 144 Bond restraints: 28197 Sorted by residual: bond pdb=" CG PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.43e+01 bond pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.08e+01 bond pdb=" CB PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 1.492 1.646 -0.154 5.00e-02 4.00e+02 9.45e+00 bond pdb=" CB ASP B1185 " pdb=" CG ASP B1185 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N PRO E 279 " pdb=" CA PRO E 279 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.67e+00 ... (remaining 28192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.40: 39401 8.40 - 16.81: 47 16.81 - 25.21: 4 25.21 - 33.62: 0 33.62 - 42.02: 1 Bond angle restraints: 39453 Sorted by residual: angle pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" C MET F 296 " ideal model delta sigma weight residual 110.80 152.82 -42.02 2.13e+00 2.20e-01 3.89e+02 angle pdb=" N LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta sigma weight residual 110.45 89.35 21.10 1.26e+00 6.30e-01 2.80e+02 angle pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" CD PRO E 279 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta sigma weight residual 110.42 89.18 21.24 1.99e+00 2.53e-01 1.14e+02 angle pdb=" N PRO E 279 " pdb=" CD PRO E 279 " pdb=" CG PRO E 279 " ideal model delta sigma weight residual 103.20 92.70 10.50 1.50e+00 4.44e-01 4.90e+01 ... (remaining 39448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 14045 35.10 - 70.20: 2008 70.20 - 105.30: 59 105.30 - 140.40: 2 140.40 - 175.50: 1 Dihedral angle restraints: 16115 sinusoidal: 8808 harmonic: 7307 Sorted by residual: dihedral pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual 122.80 147.99 -25.19 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CA LEU F 297 " pdb=" CB LEU F 297 " ideal model delta harmonic sigma weight residual 122.80 97.71 25.09 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" C MET F 296 " pdb=" N MET F 296 " pdb=" CA MET F 296 " pdb=" CB MET F 296 " ideal model delta harmonic sigma weight residual -122.60 -144.67 22.07 0 2.50e+00 1.60e-01 7.79e+01 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.335: 4353 0.335 - 0.671: 1 0.671 - 1.006: 0 1.006 - 1.341: 0 1.341 - 1.676: 1 Chirality restraints: 4355 Sorted by residual: chirality pdb=" CA MET F 296 " pdb=" N MET F 296 " pdb=" C MET F 296 " pdb=" CB MET F 296 " both_signs ideal model delta sigma weight residual False 2.51 0.83 1.68 2.00e-01 2.50e+01 7.02e+01 chirality pdb=" CA LEU F 297 " pdb=" N LEU F 297 " pdb=" C LEU F 297 " pdb=" CB LEU F 297 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA PRO E 279 " pdb=" N PRO E 279 " pdb=" C PRO E 279 " pdb=" CB PRO E 279 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4352 not shown) Planarity restraints: 3868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 278 " -0.072 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO E 279 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 279 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 279 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1175 " -0.237 9.50e-02 1.11e+02 1.07e-01 8.41e+00 pdb=" NE ARG B1175 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B1175 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B1175 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B1175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 365 " 0.019 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP D 365 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 365 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 365 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 365 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 365 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 365 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 365 " 0.000 2.00e-02 2.50e+03 ... (remaining 3865 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 111 2.49 - 3.09: 17250 3.09 - 3.70: 45778 3.70 - 4.30: 64072 4.30 - 4.90: 96689 Nonbonded interactions: 223900 Sorted by model distance: nonbonded pdb=" CD2 LEU Q 23 " pdb=" OE1 GLU Q 56 " model vdw 1.891 3.460 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 2.114 3.880 nonbonded pdb=" CD2 HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.147 1.960 nonbonded pdb=" CB HIS A 188 " pdb="ZN ZN A 501 " model vdw 2.161 2.104 nonbonded pdb=" OG1 THR A 90 " pdb=" OD1 ASN A 93 " model vdw 2.226 3.040 ... (remaining 223895 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 'D' and (resid 11 through 24 or resid 80 through 112 or resid 222 through \ 372)) selection = chain 'F' } ncs_group { reference = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = (chain 'U' and resid 11 through 116) } ncs_group { reference = (chain 'R' and resid 29 through 119) selection = chain 'V' } 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: 21.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 1.210 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 76.260 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 0.154 28199 Z= 0.180 Angle : 0.873 42.023 39455 Z= 0.451 Chirality : 0.050 1.676 4355 Planarity : 0.006 0.107 3868 Dihedral : 24.626 175.502 11388 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 0.77 % Allowed : 34.89 % Favored : 64.34 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 2433 helix: -0.96 (0.13), residues: 1333 sheet: -0.11 (0.64), residues: 84 loop : -1.79 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 365 HIS 0.019 0.001 HIS D 263 PHE 0.037 0.001 PHE B 669 TYR 0.032 0.001 TYR F 261 ARG 0.021 0.001 ARG B1175 Details of bonding type rmsd hydrogen bonds : bond 0.15861 ( 1332) hydrogen bonds : angle 5.57816 ( 3564) metal coordination : bond 0.00049 ( 1) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.70622 ( 2) covalent geometry : bond 0.00391 (28197) covalent geometry : angle 0.87299 (39453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 311 time to evaluate : 2.373 Fit side-chains revert: symmetry clash REVERT: D 223 GLN cc_start: 0.7255 (pp30) cc_final: 0.6886 (pt0) REVERT: F 296 MET cc_start: 0.3825 (mpp) cc_final: 0.2793 (mtt) REVERT: A 255 ILE cc_start: 0.3325 (mm) cc_final: 0.3005 (mm) REVERT: A 368 TYR cc_start: 0.5064 (t80) cc_final: 0.3913 (t80) REVERT: E 316 MET cc_start: 0.6508 (tpt) cc_final: 0.5929 (pmm) REVERT: G 332 ASN cc_start: 0.8113 (m-40) cc_final: 0.7504 (t0) REVERT: G 560 MET cc_start: 0.6012 (tmm) cc_final: 0.5612 (mtp) outliers start: 17 outliers final: 13 residues processed: 320 average time/residue: 0.3865 time to fit residues: 196.9844 Evaluate side-chains 291 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 278 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 261 TYR Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 247 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 HIS D 275 GLN D 350 GLN F 259 ASN O 93 GLN S 85 GLN A 331 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.144516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110624 restraints weight = 71931.468| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.28 r_work: 0.3704 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 28199 Z= 0.187 Angle : 0.602 9.033 39455 Z= 0.325 Chirality : 0.038 0.402 4355 Planarity : 0.004 0.053 3868 Dihedral : 26.363 173.687 6328 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.53 % Allowed : 28.68 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2433 helix: 0.27 (0.14), residues: 1345 sheet: -0.32 (0.60), residues: 90 loop : -1.57 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 365 HIS 0.006 0.001 HIS P 75 PHE 0.029 0.002 PHE A 160 TYR 0.028 0.002 TYR E 46 ARG 0.009 0.001 ARG R 83 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 1332) hydrogen bonds : angle 3.76626 ( 3564) metal coordination : bond 0.00363 ( 1) SS BOND : bond 0.00487 ( 1) SS BOND : angle 2.58213 ( 2) covalent geometry : bond 0.00416 (28197) covalent geometry : angle 0.60210 (39453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 326 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 223 GLN cc_start: 0.7409 (pp30) cc_final: 0.7149 (pt0) REVERT: D 395 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: F 296 MET cc_start: 0.4310 (mpp) cc_final: 0.4056 (mmt) REVERT: F 357 LYS cc_start: 0.8817 (tppt) cc_final: 0.8487 (tppt) REVERT: O 37 LYS cc_start: 0.7742 (tppp) cc_final: 0.6550 (tptp) REVERT: O 59 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: S 42 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7271 (pmm-80) REVERT: S 59 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7446 (pp20) REVERT: S 115 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8514 (mptt) REVERT: V 45 VAL cc_start: 0.7284 (m) cc_final: 0.6874 (p) REVERT: A 67 LYS cc_start: 0.6551 (pptt) cc_final: 0.6317 (ptmm) REVERT: A 88 ARG cc_start: 0.7273 (mtm110) cc_final: 0.6923 (mtm110) REVERT: A 140 ASP cc_start: 0.6705 (t0) cc_final: 0.6410 (t0) REVERT: A 172 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.5978 (tm-30) REVERT: A 199 THR cc_start: 0.6577 (p) cc_final: 0.6326 (p) REVERT: A 263 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: A 270 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: B 694 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6754 (tp40) REVERT: B 775 TRP cc_start: 0.7575 (m100) cc_final: 0.7288 (m100) REVERT: B 818 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7667 (t0) REVERT: B 890 THR cc_start: 0.3750 (OUTLIER) cc_final: 0.3404 (t) REVERT: B 1164 MET cc_start: 0.7791 (ppp) cc_final: 0.7515 (ppp) REVERT: G 560 MET cc_start: 0.6117 (tmm) cc_final: 0.5702 (mtm) outliers start: 100 outliers final: 45 residues processed: 391 average time/residue: 0.4111 time to fit residues: 253.0325 Evaluate side-chains 337 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 91 GLU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 818 ASP Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1221 HIS Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 171 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 216 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 85 GLN ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS B1222 GLN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.132724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094032 restraints weight = 68400.464| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.31 r_work: 0.3378 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 28199 Z= 0.255 Angle : 0.661 11.041 39455 Z= 0.357 Chirality : 0.042 0.232 4355 Planarity : 0.005 0.073 3868 Dihedral : 26.939 174.051 6314 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.26 % Allowed : 27.10 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2433 helix: 0.48 (0.14), residues: 1347 sheet: -0.83 (0.54), residues: 103 loop : -1.55 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 365 HIS 0.016 0.002 HIS F 330 PHE 0.019 0.002 PHE E 311 TYR 0.031 0.002 TYR E 475 ARG 0.008 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 1332) hydrogen bonds : angle 3.81117 ( 3564) metal coordination : bond 0.00373 ( 1) SS BOND : bond 0.00883 ( 1) SS BOND : angle 3.23540 ( 2) covalent geometry : bond 0.00579 (28197) covalent geometry : angle 0.66106 (39453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 337 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7942 (pm20) cc_final: 0.7563 (pm20) REVERT: D 295 ASN cc_start: 0.5189 (t0) cc_final: 0.4652 (t0) REVERT: D 305 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: D 311 LYS cc_start: 0.8554 (pttt) cc_final: 0.8181 (pttt) REVERT: D 347 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6750 (pmt) REVERT: D 395 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: F 256 MET cc_start: 0.4574 (pmm) cc_final: 0.4196 (mmm) REVERT: F 296 MET cc_start: 0.4539 (mpp) cc_final: 0.4264 (mmt) REVERT: F 363 LEU cc_start: 0.8812 (mt) cc_final: 0.8345 (tp) REVERT: P 59 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8647 (ttmt) REVERT: Q 36 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8381 (ttpp) REVERT: R 31 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6398 (ptpt) REVERT: R 90 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: S 59 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7971 (pp20) REVERT: S 73 GLU cc_start: 0.8722 (tt0) cc_final: 0.8477 (tt0) REVERT: A 88 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7584 (mtm110) REVERT: A 140 ASP cc_start: 0.6842 (t0) cc_final: 0.6487 (t0) REVERT: A 172 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 189 HIS cc_start: 0.4567 (OUTLIER) cc_final: 0.4145 (p90) REVERT: A 224 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7384 (pp) REVERT: A 235 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7398 (m-40) REVERT: A 248 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6339 (ttm-80) REVERT: B 704 GLU cc_start: 0.8117 (pp20) cc_final: 0.7733 (pp20) REVERT: B 775 TRP cc_start: 0.7663 (m100) cc_final: 0.7398 (m100) REVERT: B 860 MET cc_start: 0.6902 (mmm) cc_final: 0.5151 (tpt) REVERT: B 1164 MET cc_start: 0.8000 (ppp) cc_final: 0.7568 (ppp) REVERT: B 1257 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5413 (mmt) REVERT: E 474 VAL cc_start: 0.6271 (m) cc_final: 0.5997 (t) REVERT: G 304 ASN cc_start: 0.4123 (OUTLIER) cc_final: 0.3771 (m-40) REVERT: G 560 MET cc_start: 0.6422 (tmm) cc_final: 0.5982 (mtm) outliers start: 116 outliers final: 53 residues processed: 413 average time/residue: 0.6491 time to fit residues: 417.2233 Evaluate side-chains 360 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 59 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 999 THR Chi-restraints excluded: chain B residue 1142 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 401 TYR Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 233 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 HIS S 108 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.133629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.095623 restraints weight = 69060.555| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.30 r_work: 0.3418 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28199 Z= 0.152 Angle : 0.568 10.198 39455 Z= 0.308 Chirality : 0.037 0.294 4355 Planarity : 0.004 0.054 3868 Dihedral : 26.713 174.579 6312 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.76 % Allowed : 28.77 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2433 helix: 0.74 (0.14), residues: 1359 sheet: -1.09 (0.51), residues: 107 loop : -1.46 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 492 HIS 0.004 0.001 HIS A 151 PHE 0.015 0.001 PHE B 669 TYR 0.021 0.001 TYR B 692 ARG 0.011 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 1332) hydrogen bonds : angle 3.57906 ( 3564) metal coordination : bond 0.00070 ( 1) SS BOND : bond 0.00552 ( 1) SS BOND : angle 2.45824 ( 2) covalent geometry : bond 0.00340 (28197) covalent geometry : angle 0.56791 (39453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 261 TYR cc_start: 0.8019 (t80) cc_final: 0.7812 (t80) REVERT: D 263 HIS cc_start: 0.7442 (m-70) cc_final: 0.6920 (m170) REVERT: D 295 ASN cc_start: 0.5132 (t0) cc_final: 0.4568 (t0) REVERT: D 311 LYS cc_start: 0.8561 (pttt) cc_final: 0.8216 (pttt) REVERT: D 365 TRP cc_start: 0.8948 (t60) cc_final: 0.8743 (t60) REVERT: F 241 LYS cc_start: 0.3111 (OUTLIER) cc_final: 0.2167 (mmtm) REVERT: F 296 MET cc_start: 0.4434 (mpp) cc_final: 0.4086 (mmt) REVERT: F 309 LEU cc_start: 0.1918 (OUTLIER) cc_final: 0.1594 (tt) REVERT: P 31 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8927 (tttp) REVERT: P 59 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8588 (ttmt) REVERT: Q 36 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8311 (ttpp) REVERT: S 92 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9103 (mt) REVERT: A 40 MET cc_start: 0.5575 (tpp) cc_final: 0.5260 (tpp) REVERT: A 88 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7609 (mtm110) REVERT: A 140 ASP cc_start: 0.6884 (t0) cc_final: 0.6641 (t0) REVERT: A 172 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: A 235 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7276 (m-40) REVERT: A 315 MET cc_start: 0.7996 (mmm) cc_final: 0.7677 (mmm) REVERT: A 316 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7611 (mtm-85) REVERT: A 353 LEU cc_start: 0.8349 (tp) cc_final: 0.8108 (tt) REVERT: B 704 GLU cc_start: 0.8083 (pp20) cc_final: 0.7645 (pp20) REVERT: B 775 TRP cc_start: 0.7669 (m100) cc_final: 0.7445 (m100) REVERT: B 916 TRP cc_start: 0.7675 (m-10) cc_final: 0.7474 (m-10) REVERT: B 1164 MET cc_start: 0.8032 (ppp) cc_final: 0.7468 (ppp) REVERT: B 1257 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5298 (mmt) REVERT: E 474 VAL cc_start: 0.6132 (m) cc_final: 0.5904 (t) REVERT: G 304 ASN cc_start: 0.4082 (OUTLIER) cc_final: 0.3706 (m-40) outliers start: 83 outliers final: 50 residues processed: 376 average time/residue: 0.4256 time to fit residues: 247.3810 Evaluate side-chains 356 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 59 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 304 ASN Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 120 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 155 optimal weight: 0.0770 chunk 272 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.130366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093427 restraints weight = 68015.896| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.23 r_work: 0.3326 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28199 Z= 0.201 Angle : 0.596 12.313 39455 Z= 0.325 Chirality : 0.039 0.299 4355 Planarity : 0.004 0.092 3868 Dihedral : 26.833 176.008 6310 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.26 % Allowed : 27.41 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2433 helix: 0.80 (0.14), residues: 1359 sheet: -1.21 (0.51), residues: 105 loop : -1.37 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1151 HIS 0.007 0.001 HIS A 151 PHE 0.017 0.001 PHE A 208 TYR 0.017 0.002 TYR A 211 ARG 0.010 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1332) hydrogen bonds : angle 3.58081 ( 3564) metal coordination : bond 0.00256 ( 1) SS BOND : bond 0.00561 ( 1) SS BOND : angle 2.55273 ( 2) covalent geometry : bond 0.00457 (28197) covalent geometry : angle 0.59583 (39453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 310 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 261 TYR cc_start: 0.7963 (t80) cc_final: 0.7755 (t80) REVERT: D 295 ASN cc_start: 0.5556 (t0) cc_final: 0.4991 (t0) REVERT: D 311 LYS cc_start: 0.8585 (pttt) cc_final: 0.8247 (pttt) REVERT: D 347 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6379 (pmt) REVERT: F 241 LYS cc_start: 0.3054 (OUTLIER) cc_final: 0.2073 (mmtm) REVERT: F 296 MET cc_start: 0.4327 (mpp) cc_final: 0.3993 (mmt) REVERT: F 309 LEU cc_start: 0.1509 (OUTLIER) cc_final: 0.1147 (tt) REVERT: F 363 LEU cc_start: 0.8679 (mp) cc_final: 0.8219 (tp) REVERT: P 31 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8913 (tttp) REVERT: Q 36 LYS cc_start: 0.8705 (ptmt) cc_final: 0.8413 (ttpp) REVERT: R 31 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6496 (ptpt) REVERT: R 90 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: S 59 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7961 (pp20) REVERT: T 92 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8344 (ptm160) REVERT: U 16 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8982 (p) REVERT: A 88 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7767 (mtm110) REVERT: A 140 ASP cc_start: 0.7298 (t0) cc_final: 0.6716 (t0) REVERT: A 172 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: A 189 HIS cc_start: 0.4753 (OUTLIER) cc_final: 0.4256 (p90) REVERT: A 235 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7223 (m-40) REVERT: A 270 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 315 MET cc_start: 0.7975 (mmm) cc_final: 0.7630 (mmm) REVERT: A 338 LEU cc_start: 0.7753 (tp) cc_final: 0.7451 (tp) REVERT: A 344 TYR cc_start: 0.7887 (t80) cc_final: 0.7674 (t80) REVERT: A 353 LEU cc_start: 0.8613 (tp) cc_final: 0.8258 (tt) REVERT: A 420 TYR cc_start: 0.7498 (t80) cc_final: 0.7212 (t80) REVERT: B 704 GLU cc_start: 0.8222 (pp20) cc_final: 0.7860 (pp20) REVERT: B 775 TRP cc_start: 0.7748 (m100) cc_final: 0.7514 (m100) REVERT: B 809 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6977 (ptpt) REVERT: B 912 TRP cc_start: 0.8248 (m100) cc_final: 0.7726 (m100) REVERT: B 1016 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 1161 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6131 (tt) REVERT: B 1164 MET cc_start: 0.7927 (ppp) cc_final: 0.7453 (ppp) REVERT: B 1257 MET cc_start: 0.5821 (OUTLIER) cc_final: 0.5423 (mmt) REVERT: G 560 MET cc_start: 0.6282 (tmm) cc_final: 0.5796 (mtm) outliers start: 94 outliers final: 55 residues processed: 371 average time/residue: 0.4066 time to fit residues: 233.7222 Evaluate side-chains 366 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 294 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 289 PHE Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 58 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 227 optimal weight: 0.4980 chunk 220 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN R 64 ASN A 341 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.130841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092649 restraints weight = 68254.887| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.22 r_work: 0.3362 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28199 Z= 0.158 Angle : 0.571 11.004 39455 Z= 0.311 Chirality : 0.038 0.296 4355 Planarity : 0.004 0.086 3868 Dihedral : 26.773 175.379 6306 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.08 % Allowed : 27.46 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2433 helix: 0.94 (0.14), residues: 1355 sheet: -1.22 (0.51), residues: 105 loop : -1.30 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 916 HIS 0.004 0.001 HIS B 785 PHE 0.020 0.001 PHE A 160 TYR 0.023 0.001 TYR T 88 ARG 0.013 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 1332) hydrogen bonds : angle 3.51336 ( 3564) metal coordination : bond 0.00102 ( 1) SS BOND : bond 0.00564 ( 1) SS BOND : angle 2.39607 ( 2) covalent geometry : bond 0.00354 (28197) covalent geometry : angle 0.57067 (39453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 318 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 261 TYR cc_start: 0.7898 (t80) cc_final: 0.7648 (t80) REVERT: D 295 ASN cc_start: 0.5449 (t0) cc_final: 0.4928 (t0) REVERT: D 311 LYS cc_start: 0.8562 (pttt) cc_final: 0.8225 (pttt) REVERT: D 347 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6336 (pmt) REVERT: F 241 LYS cc_start: 0.3001 (OUTLIER) cc_final: 0.2067 (mmtm) REVERT: F 296 MET cc_start: 0.4370 (mpp) cc_final: 0.4019 (mmt) REVERT: F 309 LEU cc_start: 0.1995 (OUTLIER) cc_final: 0.1669 (tt) REVERT: F 363 LEU cc_start: 0.8693 (mp) cc_final: 0.8211 (tp) REVERT: P 31 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8917 (tttp) REVERT: P 59 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8569 (ttmt) REVERT: Q 36 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8357 (ttpp) REVERT: R 31 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6518 (ptpt) REVERT: R 90 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: R 105 LYS cc_start: 0.9103 (pptt) cc_final: 0.8875 (pttp) REVERT: S 92 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9109 (mt) REVERT: T 92 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8343 (ptm160) REVERT: U 16 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8937 (p) REVERT: A 88 ARG cc_start: 0.8090 (mtm110) cc_final: 0.7763 (mtm110) REVERT: A 140 ASP cc_start: 0.7293 (t0) cc_final: 0.6788 (t0) REVERT: A 172 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6502 (tm-30) REVERT: A 189 HIS cc_start: 0.4671 (OUTLIER) cc_final: 0.4201 (p90) REVERT: A 235 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7350 (m-40) REVERT: A 269 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7673 (tp) REVERT: A 315 MET cc_start: 0.7917 (mmm) cc_final: 0.7656 (mmm) REVERT: A 338 LEU cc_start: 0.7771 (tp) cc_final: 0.7449 (tp) REVERT: A 341 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7201 (p0) REVERT: A 353 LEU cc_start: 0.8630 (tp) cc_final: 0.8276 (tt) REVERT: A 420 TYR cc_start: 0.7670 (t80) cc_final: 0.7357 (t80) REVERT: B 704 GLU cc_start: 0.8180 (pp20) cc_final: 0.7863 (pp20) REVERT: B 775 TRP cc_start: 0.7812 (m100) cc_final: 0.7583 (m100) REVERT: B 809 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6984 (ptpt) REVERT: B 912 TRP cc_start: 0.8238 (m100) cc_final: 0.7795 (m100) REVERT: B 1016 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7996 (t80) REVERT: B 1164 MET cc_start: 0.7879 (ppp) cc_final: 0.7418 (ppp) REVERT: B 1257 MET cc_start: 0.5811 (OUTLIER) cc_final: 0.5427 (mmt) REVERT: G 560 MET cc_start: 0.6395 (tmm) cc_final: 0.5872 (mtm) outliers start: 90 outliers final: 54 residues processed: 374 average time/residue: 0.4264 time to fit residues: 244.3806 Evaluate side-chains 368 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 296 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 59 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 16 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 37 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 HIS ** V 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.123500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.085277 restraints weight = 67606.428| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.28 r_work: 0.3156 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 28199 Z= 0.390 Angle : 0.764 17.413 39455 Z= 0.416 Chirality : 0.048 0.288 4355 Planarity : 0.005 0.104 3868 Dihedral : 27.667 176.673 6306 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.30 % Allowed : 26.51 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2433 helix: 0.41 (0.14), residues: 1359 sheet: -1.73 (0.49), residues: 104 loop : -1.49 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 916 HIS 0.009 0.002 HIS R 46 PHE 0.035 0.002 PHE A 160 TYR 0.028 0.003 TYR A 211 ARG 0.014 0.001 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.05852 ( 1332) hydrogen bonds : angle 3.97956 ( 3564) metal coordination : bond 0.00958 ( 1) SS BOND : bond 0.00533 ( 1) SS BOND : angle 2.47772 ( 2) covalent geometry : bond 0.00892 (28197) covalent geometry : angle 0.76343 (39453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 309 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 261 TYR cc_start: 0.7913 (t80) cc_final: 0.7587 (t80) REVERT: D 295 ASN cc_start: 0.6244 (t0) cc_final: 0.5826 (t0) REVERT: D 324 ARG cc_start: 0.7580 (mmt-90) cc_final: 0.7158 (mmt-90) REVERT: D 347 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6339 (pmt) REVERT: D 360 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: F 256 MET cc_start: 0.4514 (pmm) cc_final: 0.3914 (ptt) REVERT: F 296 MET cc_start: 0.4578 (mpp) cc_final: 0.4184 (mmt) REVERT: F 309 LEU cc_start: 0.2059 (OUTLIER) cc_final: 0.1725 (tt) REVERT: O 37 LYS cc_start: 0.8104 (tppt) cc_final: 0.7656 (tppt) REVERT: P 31 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8983 (tttp) REVERT: Q 36 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8564 (ttpp) REVERT: R 31 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6702 (ptpt) REVERT: R 90 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: S 59 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: S 115 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8888 (mptt) REVERT: U 115 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9010 (mp) REVERT: V 39 TYR cc_start: 0.8763 (t80) cc_final: 0.8449 (t80) REVERT: V 73 GLU cc_start: 0.8952 (tp30) cc_final: 0.8724 (tp30) REVERT: A 88 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8205 (mtm110) REVERT: A 172 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: A 186 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6052 (p0) REVERT: A 213 GLU cc_start: 0.7907 (tp30) cc_final: 0.7195 (tm-30) REVERT: A 270 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: A 338 LEU cc_start: 0.8344 (tp) cc_final: 0.8086 (tp) REVERT: A 341 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7402 (p0) REVERT: A 353 LEU cc_start: 0.8767 (tp) cc_final: 0.8447 (tt) REVERT: B 704 GLU cc_start: 0.8528 (pp20) cc_final: 0.8115 (pp20) REVERT: B 722 ASN cc_start: 0.8149 (m110) cc_final: 0.7832 (m-40) REVERT: B 775 TRP cc_start: 0.7929 (m100) cc_final: 0.7661 (m100) REVERT: B 809 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7660 (ptpt) REVERT: B 1161 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6477 (tt) REVERT: B 1164 MET cc_start: 0.7940 (ppp) cc_final: 0.7501 (ppp) REVERT: B 1257 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5683 (mmt) REVERT: E 262 PHE cc_start: 0.6849 (t80) cc_final: 0.6615 (t80) REVERT: G 560 MET cc_start: 0.6700 (tmm) cc_final: 0.6172 (mtm) outliers start: 117 outliers final: 69 residues processed: 389 average time/residue: 0.4253 time to fit residues: 253.3311 Evaluate side-chains 370 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 284 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 352 CYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 115 LYS Chi-restraints excluded: chain S residue 124 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1319 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 213 optimal weight: 5.9990 chunk 241 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN A 330 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.126709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089659 restraints weight = 67559.140| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.19 r_work: 0.3258 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28199 Z= 0.176 Angle : 0.627 10.602 39455 Z= 0.341 Chirality : 0.040 0.290 4355 Planarity : 0.004 0.085 3868 Dihedral : 27.309 176.477 6302 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.72 % Allowed : 28.09 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2433 helix: 0.70 (0.14), residues: 1359 sheet: -1.70 (0.50), residues: 93 loop : -1.42 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 916 HIS 0.013 0.001 HIS E 283 PHE 0.023 0.002 PHE A 208 TYR 0.030 0.002 TYR A 211 ARG 0.015 0.001 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1332) hydrogen bonds : angle 3.72081 ( 3564) metal coordination : bond 0.00045 ( 1) SS BOND : bond 0.00582 ( 1) SS BOND : angle 2.35939 ( 2) covalent geometry : bond 0.00399 (28197) covalent geometry : angle 0.62719 (39453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 320 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.6057 (t0) cc_final: 0.5695 (t0) REVERT: D 305 GLN cc_start: 0.7831 (tp40) cc_final: 0.7570 (tp-100) REVERT: D 311 LYS cc_start: 0.8697 (pttt) cc_final: 0.8408 (ptpt) REVERT: D 324 ARG cc_start: 0.7559 (mmt-90) cc_final: 0.7118 (mmt-90) REVERT: D 347 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6305 (pmt) REVERT: F 88 TRP cc_start: 0.4014 (OUTLIER) cc_final: 0.3704 (m-90) REVERT: F 241 LYS cc_start: 0.2986 (OUTLIER) cc_final: 0.2041 (mmtm) REVERT: F 256 MET cc_start: 0.4499 (pmm) cc_final: 0.3888 (ptt) REVERT: F 296 MET cc_start: 0.4546 (mpp) cc_final: 0.4119 (mmt) REVERT: F 309 LEU cc_start: 0.2168 (OUTLIER) cc_final: 0.1860 (tt) REVERT: F 363 LEU cc_start: 0.8669 (mp) cc_final: 0.8276 (tt) REVERT: O 37 LYS cc_start: 0.8063 (tppt) cc_final: 0.7633 (tppt) REVERT: O 87 SER cc_start: 0.9266 (t) cc_final: 0.9058 (p) REVERT: P 31 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8970 (tttp) REVERT: Q 36 LYS cc_start: 0.8755 (ptmt) cc_final: 0.8455 (ttpp) REVERT: Q 114 VAL cc_start: 0.9394 (p) cc_final: 0.9170 (m) REVERT: R 31 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.6736 (pttt) REVERT: R 90 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: R 105 LYS cc_start: 0.9132 (pptt) cc_final: 0.8859 (pttp) REVERT: T 92 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8463 (ptm160) REVERT: U 29 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: A 88 ARG cc_start: 0.8324 (mtm110) cc_final: 0.8060 (mtm110) REVERT: A 134 LEU cc_start: 0.8514 (mp) cc_final: 0.8255 (mp) REVERT: A 213 GLU cc_start: 0.7364 (tp30) cc_final: 0.6765 (tm-30) REVERT: A 353 LEU cc_start: 0.8803 (tp) cc_final: 0.8490 (tt) REVERT: A 420 TYR cc_start: 0.7846 (t80) cc_final: 0.7561 (t80) REVERT: B 704 GLU cc_start: 0.8491 (pp20) cc_final: 0.8045 (pp20) REVERT: B 722 ASN cc_start: 0.8148 (m110) cc_final: 0.7867 (m-40) REVERT: B 775 TRP cc_start: 0.7936 (m100) cc_final: 0.7646 (m100) REVERT: B 809 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7563 (ptpt) REVERT: B 912 TRP cc_start: 0.8421 (m100) cc_final: 0.7943 (m100) REVERT: B 975 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8001 (tt) REVERT: B 1164 MET cc_start: 0.7925 (ppp) cc_final: 0.7537 (ppp) REVERT: B 1194 MET cc_start: 0.7417 (pmm) cc_final: 0.7077 (pmm) REVERT: B 1257 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5305 (tpp) REVERT: G 560 MET cc_start: 0.6650 (tmm) cc_final: 0.6171 (mtm) outliers start: 82 outliers final: 47 residues processed: 373 average time/residue: 0.4337 time to fit residues: 249.1344 Evaluate side-chains 362 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 303 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 228 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 200 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.126860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.090133 restraints weight = 67758.289| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.28 r_work: 0.3263 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28199 Z= 0.172 Angle : 0.619 11.895 39455 Z= 0.336 Chirality : 0.039 0.283 4355 Planarity : 0.004 0.083 3868 Dihedral : 27.107 177.089 6302 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.35 % Allowed : 28.45 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2433 helix: 0.78 (0.14), residues: 1359 sheet: -1.69 (0.50), residues: 93 loop : -1.38 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 916 HIS 0.010 0.001 HIS B 785 PHE 0.039 0.001 PHE B1017 TYR 0.028 0.002 TYR A 211 ARG 0.016 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 1332) hydrogen bonds : angle 3.65400 ( 3564) metal coordination : bond 0.00134 ( 1) SS BOND : bond 0.00591 ( 1) SS BOND : angle 2.35887 ( 2) covalent geometry : bond 0.00390 (28197) covalent geometry : angle 0.61905 (39453) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 317 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 243 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7780 (mmtp) REVERT: D 261 TYR cc_start: 0.7931 (t80) cc_final: 0.7568 (t80) REVERT: D 295 ASN cc_start: 0.6091 (t0) cc_final: 0.5713 (t0) REVERT: D 305 GLN cc_start: 0.7839 (tp40) cc_final: 0.7589 (tp-100) REVERT: D 311 LYS cc_start: 0.8680 (pttt) cc_final: 0.8410 (ptpt) REVERT: D 324 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7129 (mmt-90) REVERT: D 347 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6257 (pmt) REVERT: F 88 TRP cc_start: 0.3919 (OUTLIER) cc_final: 0.3654 (m-90) REVERT: F 241 LYS cc_start: 0.3025 (OUTLIER) cc_final: 0.2119 (mmtm) REVERT: F 256 MET cc_start: 0.4607 (pmm) cc_final: 0.4021 (ptt) REVERT: F 296 MET cc_start: 0.4706 (mpp) cc_final: 0.4250 (mmt) REVERT: F 309 LEU cc_start: 0.2199 (OUTLIER) cc_final: 0.1914 (tp) REVERT: F 363 LEU cc_start: 0.8702 (mp) cc_final: 0.8267 (tt) REVERT: P 31 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8994 (tttp) REVERT: Q 36 LYS cc_start: 0.8718 (ptmt) cc_final: 0.8423 (ttpp) REVERT: Q 114 VAL cc_start: 0.9384 (p) cc_final: 0.9158 (m) REVERT: R 31 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.6733 (pttt) REVERT: R 90 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: R 105 LYS cc_start: 0.9138 (pptt) cc_final: 0.8866 (pttp) REVERT: T 92 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8528 (ptm160) REVERT: U 29 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8124 (ttp80) REVERT: A 134 LEU cc_start: 0.8564 (mp) cc_final: 0.8282 (mp) REVERT: A 213 GLU cc_start: 0.7347 (tp30) cc_final: 0.6736 (tm-30) REVERT: A 235 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7391 (m-40) REVERT: A 353 LEU cc_start: 0.8707 (tp) cc_final: 0.8446 (tt) REVERT: A 420 TYR cc_start: 0.7908 (t80) cc_final: 0.7625 (t80) REVERT: B 704 GLU cc_start: 0.8529 (pp20) cc_final: 0.8031 (pp20) REVERT: B 722 ASN cc_start: 0.8173 (m110) cc_final: 0.7886 (m-40) REVERT: B 775 TRP cc_start: 0.7946 (m100) cc_final: 0.7640 (m100) REVERT: B 809 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7610 (ptpt) REVERT: B 912 TRP cc_start: 0.8407 (m100) cc_final: 0.7925 (m100) REVERT: B 975 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7932 (tt) REVERT: B 1164 MET cc_start: 0.7926 (ppp) cc_final: 0.7481 (ppp) REVERT: B 1194 MET cc_start: 0.7383 (pmm) cc_final: 0.7082 (pmm) REVERT: B 1257 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5463 (tpp) REVERT: G 560 MET cc_start: 0.6721 (tmm) cc_final: 0.6202 (mtm) outliers start: 74 outliers final: 51 residues processed: 365 average time/residue: 0.4662 time to fit residues: 264.1348 Evaluate side-chains 370 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 231 optimal weight: 0.0370 chunk 254 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 269 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN E 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.127632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.091305 restraints weight = 67534.150| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.26 r_work: 0.3291 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28199 Z= 0.158 Angle : 0.618 11.304 39455 Z= 0.335 Chirality : 0.039 0.288 4355 Planarity : 0.004 0.082 3868 Dihedral : 26.984 176.438 6302 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.15 % Rotamer: Outliers : 3.49 % Allowed : 28.50 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.17), residues: 2433 helix: 0.85 (0.14), residues: 1359 sheet: -1.61 (0.50), residues: 93 loop : -1.36 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 916 HIS 0.010 0.001 HIS B 785 PHE 0.035 0.001 PHE B1017 TYR 0.024 0.001 TYR A 211 ARG 0.016 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1332) hydrogen bonds : angle 3.62509 ( 3564) metal coordination : bond 0.00071 ( 1) SS BOND : bond 0.00605 ( 1) SS BOND : angle 2.37749 ( 2) covalent geometry : bond 0.00355 (28197) covalent geometry : angle 0.61750 (39453) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 313 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.6083 (t0) cc_final: 0.5715 (t0) REVERT: D 305 GLN cc_start: 0.7795 (tp40) cc_final: 0.7534 (tp-100) REVERT: D 311 LYS cc_start: 0.8679 (pttt) cc_final: 0.8428 (ptpt) REVERT: D 324 ARG cc_start: 0.7554 (mmt-90) cc_final: 0.7106 (mmt-90) REVERT: D 347 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6181 (pmt) REVERT: F 88 TRP cc_start: 0.4004 (OUTLIER) cc_final: 0.3782 (m-90) REVERT: F 241 LYS cc_start: 0.2993 (OUTLIER) cc_final: 0.2016 (mmtm) REVERT: F 256 MET cc_start: 0.4621 (pmm) cc_final: 0.4037 (ptt) REVERT: F 296 MET cc_start: 0.4684 (mpp) cc_final: 0.4438 (mmt) REVERT: F 309 LEU cc_start: 0.2164 (OUTLIER) cc_final: 0.1882 (tp) REVERT: F 361 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: F 363 LEU cc_start: 0.8702 (mp) cc_final: 0.8255 (tt) REVERT: P 31 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8873 (tttp) REVERT: Q 114 VAL cc_start: 0.9372 (p) cc_final: 0.9143 (m) REVERT: R 31 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.6760 (pttt) REVERT: R 90 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: R 105 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8924 (pttp) REVERT: T 92 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8523 (ptm160) REVERT: U 29 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8093 (ttp80) REVERT: V 73 GLU cc_start: 0.8922 (tp30) cc_final: 0.8415 (tp30) REVERT: V 76 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7963 (ttm110) REVERT: A 134 LEU cc_start: 0.8531 (mp) cc_final: 0.8260 (mp) REVERT: A 213 GLU cc_start: 0.7196 (tp30) cc_final: 0.6596 (tm-30) REVERT: A 235 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: A 353 LEU cc_start: 0.8652 (tp) cc_final: 0.8389 (tt) REVERT: A 375 ASN cc_start: 0.7430 (t0) cc_final: 0.7036 (m110) REVERT: A 420 TYR cc_start: 0.7875 (t80) cc_final: 0.7620 (t80) REVERT: B 704 GLU cc_start: 0.8511 (pp20) cc_final: 0.8024 (pp20) REVERT: B 722 ASN cc_start: 0.8164 (m110) cc_final: 0.7882 (m-40) REVERT: B 775 TRP cc_start: 0.7943 (m100) cc_final: 0.7635 (m100) REVERT: B 912 TRP cc_start: 0.8384 (m100) cc_final: 0.7899 (m100) REVERT: B 975 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7944 (tt) REVERT: B 1164 MET cc_start: 0.7870 (ppp) cc_final: 0.7465 (ppp) REVERT: B 1194 MET cc_start: 0.7354 (pmm) cc_final: 0.7053 (pmm) REVERT: B 1257 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5495 (tpp) REVERT: G 560 MET cc_start: 0.6704 (tmm) cc_final: 0.6206 (mtm) outliers start: 77 outliers final: 57 residues processed: 362 average time/residue: 0.4296 time to fit residues: 241.0450 Evaluate side-chains 375 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain F residue 88 TRP Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain P residue 31 LYS Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 29 ARG Chi-restraints excluded: chain U residue 36 LYS Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain A residue 34 TYR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1016 TYR Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain E residue 314 ASN Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 549 TYR Chi-restraints excluded: chain G residue 346 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 33 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 267 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.126460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089603 restraints weight = 67694.556| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.25 r_work: 0.3250 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28199 Z= 0.202 Angle : 0.638 12.752 39455 Z= 0.345 Chirality : 0.040 0.265 4355 Planarity : 0.004 0.086 3868 Dihedral : 27.056 176.347 6302 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 94.99 % Rotamer: Outliers : 3.62 % Allowed : 28.41 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2433 helix: 0.86 (0.14), residues: 1343 sheet: -1.67 (0.51), residues: 93 loop : -1.31 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 916 HIS 0.010 0.001 HIS B 785 PHE 0.033 0.002 PHE B1017 TYR 0.028 0.002 TYR A 211 ARG 0.016 0.001 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1332) hydrogen bonds : angle 3.65206 ( 3564) metal coordination : bond 0.00238 ( 1) SS BOND : bond 0.00560 ( 1) SS BOND : angle 2.36637 ( 2) covalent geometry : bond 0.00459 (28197) covalent geometry : angle 0.63824 (39453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24125.30 seconds wall clock time: 420 minutes 31.96 seconds (25231.96 seconds total)