Starting phenix.real_space_refine on Sun May 25 18:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd6_37126/05_2025/8kd6_37126.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd6_37126/05_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_37126/05_2025/8kd6_37126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd6_37126/05_2025/8kd6_37126.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd6_37126/05_2025/8kd6_37126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd6_37126/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 16.89, per 1000 atoms: 0.63 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: 7.18 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: 10.37 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: 16.03 Time building geometry restraints manager: 7.57 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: 14.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 76.450 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.150 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.940 ------------------------------------------------------------------------------- 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 : 2.464 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: 0.3762 time to fit residues: 191.3823 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 : 2.343 ------------------------------------------------------------------------------- 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 = 0.144518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.110609 restraints weight = 71934.385| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.30 r_work: 0.3703 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1952 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 0.03949 ( 1332) hydrogen bonds : angle 3.76627 ( 3564) metal coordination : bond 0.00362 ( 1) SS BOND : bond 0.00487 ( 1) SS BOND : angle 2.58163 ( 2) covalent geometry : bond 0.00416 (28197) covalent geometry : angle 0.60208 (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 : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 223 GLN cc_start: 0.7411 (pp30) cc_final: 0.7151 (pt0) REVERT: D 395 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: F 296 MET cc_start: 0.4341 (mpp) cc_final: 0.4091 (mmt) REVERT: F 357 LYS cc_start: 0.8802 (tppt) cc_final: 0.8481 (tppt) REVERT: O 37 LYS cc_start: 0.7751 (tppp) cc_final: 0.6556 (tptp) REVERT: O 59 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: S 42 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7280 (pmm-80) REVERT: S 59 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7422 (pp20) REVERT: S 115 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8524 (mptt) REVERT: V 45 VAL cc_start: 0.7278 (m) cc_final: 0.6879 (p) REVERT: A 67 LYS cc_start: 0.6563 (pptt) cc_final: 0.6321 (ptmm) REVERT: A 88 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6932 (mtm110) REVERT: A 140 ASP cc_start: 0.6704 (t0) cc_final: 0.6405 (t0) REVERT: A 160 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.5391 (t80) REVERT: A 172 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: A 199 THR cc_start: 0.6583 (p) cc_final: 0.6333 (p) REVERT: A 263 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: A 270 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: B 694 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: B 775 TRP cc_start: 0.7558 (m100) cc_final: 0.7275 (m100) REVERT: B 818 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7701 (t0) REVERT: B 890 THR cc_start: 0.3751 (OUTLIER) cc_final: 0.3402 (t) REVERT: B 1164 MET cc_start: 0.7819 (ppp) cc_final: 0.7544 (ppp) REVERT: G 560 MET cc_start: 0.6119 (tmm) cc_final: 0.5701 (mtm) outliers start: 100 outliers final: 45 residues processed: 391 average time/residue: 0.3756 time to fit residues: 230.2373 Evaluate side-chains 339 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 2.389 ------------------------------------------------------------------------------- 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 160 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: 3.9990 chunk 141 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 216 optimal weight: 0.5980 chunk 253 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 HIS F 263 HIS S 85 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.130976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091861 restraints weight = 68147.541| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.30 r_work: 0.3338 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 28199 Z= 0.290 Angle : 0.689 10.950 39455 Z= 0.371 Chirality : 0.043 0.229 4355 Planarity : 0.005 0.089 3868 Dihedral : 27.074 174.266 6314 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.48 % Allowed : 27.00 % Favored : 67.51 % 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: -0.73 (0.16), residues: 2433 helix: 0.37 (0.14), residues: 1346 sheet: -1.13 (0.50), residues: 112 loop : -1.56 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1151 HIS 0.006 0.001 HIS A 188 PHE 0.033 0.002 PHE A 160 TYR 0.023 0.002 TYR A 211 ARG 0.009 0.001 ARG R 83 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1332) hydrogen bonds : angle 3.88559 ( 3564) metal coordination : bond 0.00665 ( 1) SS BOND : bond 0.00803 ( 1) SS BOND : angle 3.62853 ( 2) covalent geometry : bond 0.00660 (28197) covalent geometry : angle 0.68850 (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 452 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 331 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 GLN cc_start: 0.7912 (pm20) cc_final: 0.7483 (pm20) REVERT: D 263 HIS cc_start: 0.7479 (m90) cc_final: 0.7019 (m170) REVERT: D 295 ASN cc_start: 0.5293 (t0) cc_final: 0.4795 (t0) REVERT: D 305 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: D 311 LYS cc_start: 0.8600 (pttt) cc_final: 0.8222 (pttt) REVERT: D 347 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6759 (pmt) REVERT: D 395 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: F 256 MET cc_start: 0.4702 (pmm) cc_final: 0.4259 (mmm) REVERT: F 296 MET cc_start: 0.4715 (mpp) cc_final: 0.4426 (mmt) REVERT: F 363 LEU cc_start: 0.8818 (mt) cc_final: 0.8345 (tp) REVERT: P 31 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8825 (tttp) REVERT: P 59 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8633 (ttmt) REVERT: Q 36 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8435 (ttpp) REVERT: R 31 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6449 (ptpt) REVERT: R 90 GLU cc_start: 0.8766 (mp0) cc_final: 0.8357 (mp0) REVERT: S 59 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7931 (pp20) REVERT: A 88 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7624 (mtm110) REVERT: A 100 GLU cc_start: 0.8183 (mp0) cc_final: 0.7960 (mt-10) REVERT: A 140 ASP cc_start: 0.6910 (t0) cc_final: 0.6378 (t0) REVERT: A 160 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5658 (t80) REVERT: A 172 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: A 189 HIS cc_start: 0.4764 (OUTLIER) cc_final: 0.4307 (p90) REVERT: A 224 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7492 (pp) REVERT: A 235 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7429 (m-40) REVERT: A 248 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6293 (ttm-80) REVERT: A 344 TYR cc_start: 0.7931 (t80) cc_final: 0.7700 (t80) REVERT: A 353 LEU cc_start: 0.8293 (tp) cc_final: 0.8033 (tt) REVERT: B 704 GLU cc_start: 0.8159 (pp20) cc_final: 0.7761 (pp20) REVERT: B 775 TRP cc_start: 0.7690 (m100) cc_final: 0.7384 (m100) REVERT: B 860 MET cc_start: 0.6854 (mmm) cc_final: 0.6154 (mmp) REVERT: B 1164 MET cc_start: 0.7927 (ppp) cc_final: 0.7499 (ppp) REVERT: B 1257 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.5487 (mmt) REVERT: E 474 VAL cc_start: 0.6557 (m) cc_final: 0.6325 (t) REVERT: E 492 TRP cc_start: 0.7251 (t60) cc_final: 0.6836 (t60) REVERT: G 304 ASN cc_start: 0.4064 (OUTLIER) cc_final: 0.3674 (m-40) REVERT: G 560 MET cc_start: 0.6398 (tmm) cc_final: 0.5938 (mtm) outliers start: 121 outliers final: 55 residues processed: 410 average time/residue: 0.4225 time to fit residues: 264.4155 Evaluate side-chains 355 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 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 31 LYS 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 64 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain R residue 31 LYS Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain S residue 58 THR 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 160 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 277 SER Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 369 LEU 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 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 273 LEU Chi-restraints excluded: chain E residue 305 GLU 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 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: 0.7980 chunk 57 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 167 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 245 optimal weight: 0.0670 chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 64 ASN 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 = 0.4285 r_free = 0.4285 target = 0.134129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.096571 restraints weight = 69250.345| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.25 r_work: 0.3438 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28199 Z= 0.130 Angle : 0.573 10.717 39455 Z= 0.310 Chirality : 0.037 0.267 4355 Planarity : 0.004 0.054 3868 Dihedral : 26.734 174.806 6308 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.76 % Allowed : 28.23 % 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: -0.37 (0.17), residues: 2433 helix: 0.71 (0.14), residues: 1359 sheet: -1.09 (0.52), residues: 106 loop : -1.50 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 301 HIS 0.005 0.001 HIS A 151 PHE 0.030 0.001 PHE A 160 TYR 0.016 0.001 TYR V 37 ARG 0.010 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 1332) hydrogen bonds : angle 3.58516 ( 3564) metal coordination : bond 0.00092 ( 1) SS BOND : bond 0.00621 ( 1) SS BOND : angle 2.35637 ( 2) covalent geometry : bond 0.00282 (28197) covalent geometry : angle 0.57300 (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 414 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 2.691 Fit side-chains revert: symmetry clash REVERT: D 263 HIS cc_start: 0.7577 (m90) cc_final: 0.7155 (m170) REVERT: D 295 ASN cc_start: 0.5017 (t0) cc_final: 0.4497 (t0) REVERT: D 311 LYS cc_start: 0.8552 (pttt) cc_final: 0.8211 (pttt) REVERT: F 241 LYS cc_start: 0.3080 (OUTLIER) cc_final: 0.2114 (mmtm) REVERT: F 296 MET cc_start: 0.4347 (mpp) cc_final: 0.4005 (mmt) REVERT: F 309 LEU cc_start: 0.2028 (OUTLIER) cc_final: 0.1719 (tt) REVERT: P 31 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8872 (tttp) REVERT: P 59 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8564 (ttmt) REVERT: R 90 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8429 (mp0) REVERT: S 92 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9045 (mt) REVERT: A 88 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7439 (mtm110) REVERT: A 100 GLU cc_start: 0.8105 (mp0) cc_final: 0.7870 (mt-10) REVERT: A 160 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.5447 (t80) REVERT: A 172 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: A 189 HIS cc_start: 0.4462 (OUTLIER) cc_final: 0.3889 (p90) REVERT: A 235 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7019 (m-40) REVERT: A 316 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7620 (mtm-85) REVERT: A 353 LEU cc_start: 0.8410 (tp) cc_final: 0.8143 (tt) REVERT: B 704 GLU cc_start: 0.8087 (pp20) cc_final: 0.7795 (pp20) REVERT: B 775 TRP cc_start: 0.7649 (m100) cc_final: 0.7404 (m100) REVERT: B 1164 MET cc_start: 0.7956 (ppp) cc_final: 0.7480 (ppp) REVERT: B 1257 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5260 (mmt) REVERT: E 474 VAL cc_start: 0.6242 (m) cc_final: 0.6024 (t) REVERT: G 304 ASN cc_start: 0.4064 (OUTLIER) cc_final: 0.3625 (m-40) outliers start: 83 outliers final: 47 residues processed: 384 average time/residue: 0.4127 time to fit residues: 244.7961 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 : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 334 LEU 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 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 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 Q residue 115 LEU Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 42 ARG 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 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 160 PHE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 189 HIS 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 341 PHE Chi-restraints excluded: chain E residue 360 THR 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 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: 0.4980 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 25 ASN T 75 HIS A 72 GLN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.128320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088977 restraints weight = 67759.543| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.27 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 28199 Z= 0.262 Angle : 0.645 14.021 39455 Z= 0.349 Chirality : 0.042 0.305 4355 Planarity : 0.005 0.113 3868 Dihedral : 27.041 176.336 6306 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.76 % Allowed : 27.00 % Favored : 68.24 % 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: -0.33 (0.17), residues: 2433 helix: 0.75 (0.14), residues: 1354 sheet: -1.30 (0.51), residues: 104 loop : -1.45 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 492 HIS 0.006 0.001 HIS R 46 PHE 0.031 0.002 PHE A 160 TYR 0.019 0.002 TYR A 211 ARG 0.013 0.001 ARG B1175 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 1332) hydrogen bonds : angle 3.68801 ( 3564) metal coordination : bond 0.00369 ( 1) SS BOND : bond 0.00587 ( 1) SS BOND : angle 2.54983 ( 2) covalent geometry : bond 0.00596 (28197) covalent geometry : angle 0.64520 (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 417 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 312 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5560 (t0) cc_final: 0.5000 (t0) REVERT: D 305 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: D 311 LYS cc_start: 0.8619 (pttt) cc_final: 0.8282 (pttt) REVERT: D 347 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6292 (pmt) REVERT: F 241 LYS cc_start: 0.3036 (OUTLIER) cc_final: 0.2116 (mmtm) REVERT: F 296 MET cc_start: 0.4375 (mpp) cc_final: 0.4051 (mmt) REVERT: F 309 LEU cc_start: 0.1685 (OUTLIER) cc_final: 0.1348 (tt) REVERT: F 363 LEU cc_start: 0.8667 (mp) cc_final: 0.8191 (tp) REVERT: P 31 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8890 (tttp) REVERT: Q 36 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8407 (ttpp) REVERT: R 31 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.6597 (ptpt) REVERT: R 90 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: S 59 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: U 16 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8995 (p) REVERT: A 72 GLN cc_start: 0.8441 (tt0) cc_final: 0.8022 (tt0) REVERT: A 88 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7812 (mtm110) REVERT: A 100 GLU cc_start: 0.8170 (mp0) cc_final: 0.7894 (mt-10) REVERT: A 160 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5765 (t80) REVERT: A 172 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: A 189 HIS cc_start: 0.4965 (OUTLIER) cc_final: 0.4434 (p90) REVERT: A 213 GLU cc_start: 0.7156 (tp30) cc_final: 0.6339 (tm-30) REVERT: A 269 LEU cc_start: 0.7774 (tp) cc_final: 0.7529 (tp) REVERT: A 270 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: A 280 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6887 (ttm170) REVERT: A 353 LEU cc_start: 0.8664 (tp) cc_final: 0.8295 (tt) REVERT: B 704 GLU cc_start: 0.8298 (pp20) cc_final: 0.7960 (pp20) REVERT: B 775 TRP cc_start: 0.7768 (m100) cc_final: 0.7496 (m100) REVERT: B 809 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7129 (ptpt) REVERT: B 912 TRP cc_start: 0.8308 (m100) cc_final: 0.7812 (m100) REVERT: B 1164 MET cc_start: 0.7916 (ppp) cc_final: 0.7457 (ppp) REVERT: B 1257 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5401 (mmt) REVERT: B 1289 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: G 560 MET cc_start: 0.6295 (tmm) cc_final: 0.5790 (mtm) outliers start: 105 outliers final: 55 residues processed: 376 average time/residue: 0.3961 time to fit residues: 229.8460 Evaluate side-chains 368 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 295 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 305 GLN Chi-restraints excluded: chain D residue 334 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 345 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 73 GLU 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 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 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 160 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 270 GLN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 280 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 369 LEU 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 934 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 B residue 1289 GLN Chi-restraints excluded: chain E residue 305 GLU 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: 3.9990 chunk 236 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 0.0030 chunk 124 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN A 235 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** E 314 ASN ** 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 = 0.4232 r_free = 0.4232 target = 0.130459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.093725 restraints weight = 68142.891| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.22 r_work: 0.3341 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28199 Z= 0.147 Angle : 0.573 9.431 39455 Z= 0.312 Chirality : 0.037 0.297 4355 Planarity : 0.004 0.083 3868 Dihedral : 26.846 175.628 6306 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.21 % Allowed : 27.28 % Favored : 68.51 % 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: -0.14 (0.17), residues: 2433 helix: 0.92 (0.14), residues: 1355 sheet: -1.34 (0.50), residues: 106 loop : -1.38 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 916 HIS 0.006 0.001 HIS A 43 PHE 0.030 0.001 PHE A 160 TYR 0.018 0.001 TYR A 347 ARG 0.014 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1332) hydrogen bonds : angle 3.52408 ( 3564) metal coordination : bond 0.00037 ( 1) SS BOND : bond 0.00579 ( 1) SS BOND : angle 2.35089 ( 2) covalent geometry : bond 0.00326 (28197) covalent geometry : angle 0.57228 (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 410 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 317 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5507 (t0) cc_final: 0.4994 (t0) REVERT: D 347 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6358 (pmt) REVERT: F 241 LYS cc_start: 0.3038 (OUTLIER) cc_final: 0.2089 (mmtm) REVERT: F 296 MET cc_start: 0.4416 (mpp) cc_final: 0.4087 (mmt) REVERT: F 309 LEU cc_start: 0.2062 (OUTLIER) cc_final: 0.1758 (tt) REVERT: F 363 LEU cc_start: 0.8709 (mp) cc_final: 0.8233 (tp) REVERT: O 37 LYS cc_start: 0.7931 (tppt) cc_final: 0.7528 (tppt) REVERT: P 31 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8847 (tttp) REVERT: R 31 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6537 (ptpt) REVERT: R 90 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: R 105 LYS cc_start: 0.9094 (pptt) cc_final: 0.8862 (pttp) REVERT: S 92 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9092 (mt) REVERT: T 92 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8374 (ptm160) REVERT: U 16 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8968 (p) REVERT: U 51 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8859 (tp) REVERT: A 88 ARG cc_start: 0.8110 (mtm110) cc_final: 0.7827 (mtm110) REVERT: A 160 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5692 (t80) REVERT: A 189 HIS cc_start: 0.4894 (OUTLIER) cc_final: 0.4301 (p90) REVERT: A 280 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6550 (ttm170) REVERT: A 353 LEU cc_start: 0.8652 (tp) cc_final: 0.8185 (tt) REVERT: A 420 TYR cc_start: 0.7591 (t80) cc_final: 0.7302 (t80) REVERT: B 704 GLU cc_start: 0.8329 (pp20) cc_final: 0.7967 (pp20) REVERT: B 775 TRP cc_start: 0.7810 (m100) cc_final: 0.7492 (m100) REVERT: B 809 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7057 (ptpt) REVERT: B 912 TRP cc_start: 0.8301 (m100) cc_final: 0.7847 (m100) REVERT: B 931 LEU cc_start: 0.8639 (mp) cc_final: 0.8381 (mt) REVERT: B 1016 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 1164 MET cc_start: 0.7964 (ppp) cc_final: 0.7491 (ppp) REVERT: B 1257 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5341 (mmt) REVERT: G 560 MET cc_start: 0.6426 (tmm) cc_final: 0.5875 (mtm) outliers start: 93 outliers final: 53 residues processed: 380 average time/residue: 0.4154 time to fit residues: 243.7345 Evaluate side-chains 368 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 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 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 332 LEU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 48 LEU 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 Q residue 115 LEU 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 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 62 ILE 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 160 PHE 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 280 ARG 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 1207 VAL 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 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 540 THR 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: 0.0670 chunk 234 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 330 ASN ** 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 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.092295 restraints weight = 67824.622| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.23 r_work: 0.3309 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28199 Z= 0.178 Angle : 0.590 12.615 39455 Z= 0.320 Chirality : 0.038 0.292 4355 Planarity : 0.004 0.079 3868 Dihedral : 26.868 176.208 6306 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.49 % Allowed : 27.41 % Favored : 68.10 % 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: -0.08 (0.17), residues: 2433 helix: 0.94 (0.14), residues: 1357 sheet: -1.34 (0.47), residues: 116 loop : -1.32 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 916 HIS 0.004 0.001 HIS A 43 PHE 0.029 0.001 PHE A 160 TYR 0.015 0.001 TYR A 347 ARG 0.012 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1332) hydrogen bonds : angle 3.53199 ( 3564) metal coordination : bond 0.00147 ( 1) SS BOND : bond 0.00705 ( 1) SS BOND : angle 2.48898 ( 2) covalent geometry : bond 0.00400 (28197) covalent geometry : angle 0.58974 (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 414 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 315 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5502 (t0) cc_final: 0.4069 (t0) REVERT: D 296 MET cc_start: 0.5677 (mpt) cc_final: 0.4785 (mpt) REVERT: D 311 LYS cc_start: 0.8604 (pttt) cc_final: 0.8294 (ptpt) REVERT: D 347 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6338 (pmt) REVERT: F 241 LYS cc_start: 0.3056 (OUTLIER) cc_final: 0.2149 (mmtm) REVERT: F 296 MET cc_start: 0.4545 (mpp) cc_final: 0.4147 (mmt) REVERT: F 309 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1736 (tt) REVERT: F 363 LEU cc_start: 0.8772 (mp) cc_final: 0.8298 (tp) REVERT: P 31 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8883 (tttp) REVERT: R 31 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6567 (ptpt) REVERT: R 90 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: R 105 LYS cc_start: 0.9121 (pptt) cc_final: 0.8872 (pttp) REVERT: S 115 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8873 (mptt) REVERT: T 92 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8377 (ptm160) REVERT: U 29 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8119 (ttp80) REVERT: A 72 GLN cc_start: 0.8371 (tt0) cc_final: 0.7983 (tt0) REVERT: A 88 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7906 (mtm110) REVERT: A 160 PHE cc_start: 0.6088 (OUTLIER) cc_final: 0.5683 (t80) REVERT: A 165 ASP cc_start: 0.7714 (p0) cc_final: 0.7468 (p0) REVERT: A 172 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: A 189 HIS cc_start: 0.4978 (OUTLIER) cc_final: 0.4430 (p90) REVERT: A 270 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: A 353 LEU cc_start: 0.8616 (tp) cc_final: 0.8196 (tt) REVERT: A 420 TYR cc_start: 0.7601 (t80) cc_final: 0.7341 (t80) REVERT: B 704 GLU cc_start: 0.8401 (pp20) cc_final: 0.8000 (pp20) REVERT: B 722 ASN cc_start: 0.8130 (m110) cc_final: 0.7873 (m110) REVERT: B 775 TRP cc_start: 0.7826 (m100) cc_final: 0.7495 (m100) REVERT: B 809 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7099 (ptpt) REVERT: B 912 TRP cc_start: 0.8333 (m100) cc_final: 0.7815 (m100) REVERT: B 931 LEU cc_start: 0.8716 (mp) cc_final: 0.8455 (mt) REVERT: B 1164 MET cc_start: 0.8025 (ppp) cc_final: 0.7515 (ppp) REVERT: B 1257 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5455 (mmt) REVERT: B 1289 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7978 (pp30) REVERT: G 560 MET cc_start: 0.6534 (tmm) cc_final: 0.5960 (mtm) outliers start: 99 outliers final: 57 residues processed: 381 average time/residue: 0.4050 time to fit residues: 240.0344 Evaluate side-chains 375 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 302 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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 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 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 45 THR Chi-restraints excluded: chain O residue 48 LEU 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 Q residue 115 LEU 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 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 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 97 PHE Chi-restraints excluded: chain A residue 160 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 234 VAL Chi-restraints excluded: chain A residue 270 GLN 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 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 809 LYS 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 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1289 GLN Chi-restraints excluded: chain B residue 1319 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 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 549 TYR 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: 6.9990 chunk 241 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1150 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.125150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.087444 restraints weight = 67369.590| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.26 r_work: 0.3203 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 28199 Z= 0.285 Angle : 0.674 15.307 39455 Z= 0.365 Chirality : 0.043 0.279 4355 Planarity : 0.005 0.087 3868 Dihedral : 27.369 175.686 6306 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.40 % Allowed : 27.28 % 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: -0.36 (0.17), residues: 2433 helix: 0.70 (0.14), residues: 1351 sheet: -1.50 (0.50), residues: 94 loop : -1.40 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 916 HIS 0.007 0.001 HIS A 43 PHE 0.034 0.002 PHE A 160 TYR 0.027 0.002 TYR T 88 ARG 0.013 0.001 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1332) hydrogen bonds : angle 3.77583 ( 3564) metal coordination : bond 0.00551 ( 1) SS BOND : bond 0.00575 ( 1) SS BOND : angle 2.33075 ( 2) covalent geometry : bond 0.00648 (28197) covalent geometry : angle 0.67428 (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 405 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 308 time to evaluate : 2.892 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 243 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7852 (mmtp) REVERT: D 295 ASN cc_start: 0.6010 (t0) cc_final: 0.5596 (t0) REVERT: D 324 ARG cc_start: 0.7527 (mmt-90) cc_final: 0.7093 (mmt-90) REVERT: D 347 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6329 (pmt) REVERT: D 360 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: F 88 TRP cc_start: 0.3984 (OUTLIER) cc_final: 0.3723 (m-90) REVERT: F 241 LYS cc_start: 0.2984 (OUTLIER) cc_final: 0.2013 (mmtm) REVERT: F 256 MET cc_start: 0.4642 (pmm) cc_final: 0.4009 (ptt) REVERT: F 296 MET cc_start: 0.4590 (mpp) cc_final: 0.4178 (mmt) REVERT: F 309 LEU cc_start: 0.2091 (OUTLIER) cc_final: 0.1756 (tt) REVERT: O 37 LYS cc_start: 0.8059 (tppt) cc_final: 0.7619 (tppt) REVERT: P 31 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8952 (tttp) REVERT: Q 36 LYS cc_start: 0.8755 (ptmt) cc_final: 0.8474 (ttpp) REVERT: R 31 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6702 (ptpt) REVERT: R 90 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: R 105 LYS cc_start: 0.9145 (pptt) cc_final: 0.8904 (pttp) REVERT: S 59 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7830 (pp20) REVERT: S 115 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8880 (mptt) REVERT: T 92 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8537 (ptm160) REVERT: U 29 ARG cc_start: 0.9437 (OUTLIER) cc_final: 0.8196 (ttp80) REVERT: U 115 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9041 (mp) REVERT: V 39 TYR cc_start: 0.8695 (t80) cc_final: 0.8395 (t80) REVERT: A 88 ARG cc_start: 0.8263 (mtm110) cc_final: 0.8027 (mtm110) REVERT: A 160 PHE cc_start: 0.6309 (OUTLIER) cc_final: 0.5680 (t80) REVERT: A 186 ASP cc_start: 0.6674 (OUTLIER) cc_final: 0.6024 (p0) REVERT: A 213 GLU cc_start: 0.7694 (tp30) cc_final: 0.7048 (tm-30) REVERT: A 270 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 353 LEU cc_start: 0.8714 (tp) cc_final: 0.8314 (tt) REVERT: A 420 TYR cc_start: 0.7805 (t80) cc_final: 0.7527 (t80) REVERT: B 704 GLU cc_start: 0.8561 (pp20) cc_final: 0.8128 (pp20) REVERT: B 722 ASN cc_start: 0.8121 (m110) cc_final: 0.7833 (m-40) REVERT: B 775 TRP cc_start: 0.7926 (m100) cc_final: 0.7571 (m100) REVERT: B 809 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7537 (ptpt) REVERT: B 931 LEU cc_start: 0.8858 (mp) cc_final: 0.8646 (mt) REVERT: B 1161 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6389 (tt) REVERT: B 1164 MET cc_start: 0.7978 (ppp) cc_final: 0.7477 (ppp) REVERT: B 1257 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5350 (tpp) REVERT: B 1289 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: E 262 PHE cc_start: 0.6733 (t80) cc_final: 0.6511 (t80) REVERT: E 316 MET cc_start: 0.6052 (pmm) cc_final: 0.5347 (tpt) REVERT: G 560 MET cc_start: 0.6654 (tmm) cc_final: 0.6102 (mtm) outliers start: 97 outliers final: 62 residues processed: 372 average time/residue: 0.4311 time to fit residues: 244.2320 Evaluate side-chains 373 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 291 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 360 GLU 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 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 354 LEU Chi-restraints excluded: chain O residue 48 LEU 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 71 ARG Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 115 LEU 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 115 LYS Chi-restraints excluded: chain S residue 124 ILE 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 U residue 115 LEU Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 160 PHE 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 277 SER Chi-restraints excluded: chain A residue 280 ARG 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 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 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 1250 VAL Chi-restraints excluded: chain B residue 1257 MET Chi-restraints excluded: chain B residue 1289 GLN 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 373 SER Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain E residue 540 THR 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: 8.9990 chunk 44 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 251 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 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 = 0.4184 r_free = 0.4184 target = 0.127258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090420 restraints weight = 67829.278| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.28 r_work: 0.3269 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28199 Z= 0.164 Angle : 0.619 10.839 39455 Z= 0.334 Chirality : 0.039 0.319 4355 Planarity : 0.004 0.084 3868 Dihedral : 27.134 176.311 6306 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.58 % Allowed : 28.32 % Favored : 68.10 % 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: -0.23 (0.17), residues: 2433 helix: 0.82 (0.14), residues: 1351 sheet: -1.49 (0.48), residues: 103 loop : -1.36 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 916 HIS 0.011 0.001 HIS B 785 PHE 0.033 0.001 PHE A 160 TYR 0.058 0.002 TYR T 88 ARG 0.016 0.000 ARG U 71 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 1332) hydrogen bonds : angle 3.65172 ( 3564) metal coordination : bond 0.00096 ( 1) SS BOND : bond 0.00605 ( 1) SS BOND : angle 2.37924 ( 2) covalent geometry : bond 0.00370 (28197) covalent geometry : angle 0.61833 (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 387 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 308 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5928 (t0) cc_final: 0.5524 (t0) REVERT: D 311 LYS cc_start: 0.8661 (pttt) cc_final: 0.8387 (ptpt) REVERT: D 324 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7149 (mmt-90) REVERT: D 347 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6222 (pmt) REVERT: F 241 LYS cc_start: 0.2960 (OUTLIER) cc_final: 0.2042 (mmtm) REVERT: F 256 MET cc_start: 0.4677 (pmm) cc_final: 0.4076 (ptt) REVERT: F 296 MET cc_start: 0.4700 (mpp) cc_final: 0.4246 (mmt) REVERT: F 309 LEU cc_start: 0.2203 (OUTLIER) cc_final: 0.1933 (tt) REVERT: F 363 LEU cc_start: 0.8728 (mp) cc_final: 0.8328 (tt) REVERT: O 37 LYS cc_start: 0.8035 (tppt) cc_final: 0.7593 (tppt) REVERT: P 31 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8886 (tttp) REVERT: R 31 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.6739 (pttt) REVERT: R 90 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: R 105 LYS cc_start: 0.9128 (pptt) cc_final: 0.8857 (pttp) REVERT: S 59 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: T 92 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8406 (ptm160) REVERT: U 29 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8086 (ttp80) REVERT: A 160 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5773 (t80) REVERT: A 213 GLU cc_start: 0.7285 (tp30) cc_final: 0.6809 (tm-30) REVERT: A 259 MET cc_start: 0.8140 (mmp) cc_final: 0.7889 (mmm) REVERT: A 353 LEU cc_start: 0.8642 (tp) cc_final: 0.8407 (tt) REVERT: A 373 MET cc_start: 0.7755 (mmt) cc_final: 0.7538 (mmt) REVERT: A 420 TYR cc_start: 0.7862 (t80) cc_final: 0.7590 (t80) REVERT: B 704 GLU cc_start: 0.8529 (pp20) cc_final: 0.8095 (pp20) REVERT: B 722 ASN cc_start: 0.8153 (m110) cc_final: 0.7875 (m-40) REVERT: B 775 TRP cc_start: 0.7926 (m100) cc_final: 0.7573 (m100) REVERT: B 809 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7593 (ptpt) REVERT: B 912 TRP cc_start: 0.8419 (m100) cc_final: 0.7939 (m100) REVERT: B 931 LEU cc_start: 0.8768 (mp) cc_final: 0.8555 (mt) REVERT: B 1164 MET cc_start: 0.8019 (ppp) cc_final: 0.7563 (ppp) REVERT: B 1194 MET cc_start: 0.7388 (pmm) cc_final: 0.7089 (pmm) REVERT: B 1257 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5412 (tpp) REVERT: E 316 MET cc_start: 0.6062 (pmm) cc_final: 0.5244 (tpt) REVERT: G 560 MET cc_start: 0.6709 (tmm) cc_final: 0.6167 (mtm) outliers start: 79 outliers final: 56 residues processed: 356 average time/residue: 0.4172 time to fit residues: 229.0158 Evaluate side-chains 369 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 237 GLU 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 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 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 354 LEU Chi-restraints excluded: chain O residue 48 LEU 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 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 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 160 PHE 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 246 THR 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 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 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 540 THR 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: 6.9990 chunk 254 optimal weight: 0.0040 chunk 193 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 60 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 108 ASN A 72 GLN A 330 ASN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 379 ASN ** 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 = 0.4168 r_free = 0.4168 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087268 restraints weight = 67262.928| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.19 r_work: 0.3258 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28199 Z= 0.210 Angle : 0.636 13.105 39455 Z= 0.343 Chirality : 0.040 0.270 4355 Planarity : 0.004 0.088 3868 Dihedral : 27.124 176.501 6306 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.40 % Allowed : 28.55 % Favored : 68.06 % 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: -0.23 (0.17), residues: 2433 helix: 0.84 (0.14), residues: 1350 sheet: -1.80 (0.47), residues: 103 loop : -1.34 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 916 HIS 0.009 0.001 HIS B 785 PHE 0.038 0.002 PHE B1017 TYR 0.031 0.002 TYR A 211 ARG 0.009 0.000 ARG R 83 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 1332) hydrogen bonds : angle 3.66352 ( 3564) metal coordination : bond 0.00223 ( 1) SS BOND : bond 0.00564 ( 1) SS BOND : angle 2.36309 ( 2) covalent geometry : bond 0.00478 (28197) covalent geometry : angle 0.63627 (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 385 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 310 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 295 ASN cc_start: 0.5946 (t0) cc_final: 0.5569 (t0) REVERT: D 311 LYS cc_start: 0.8677 (pttt) cc_final: 0.8431 (ptpt) REVERT: D 324 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.7090 (mmt-90) REVERT: D 347 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6253 (pmt) REVERT: D 360 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: F 241 LYS cc_start: 0.2953 (OUTLIER) cc_final: 0.2035 (mmtm) REVERT: F 256 MET cc_start: 0.4690 (pmm) cc_final: 0.4103 (ptt) REVERT: F 296 MET cc_start: 0.4690 (mpp) cc_final: 0.4220 (mmt) REVERT: F 309 LEU cc_start: 0.2204 (OUTLIER) cc_final: 0.1907 (tp) REVERT: F 363 LEU cc_start: 0.8755 (mp) cc_final: 0.8309 (tt) REVERT: O 37 LYS cc_start: 0.8094 (tppt) cc_final: 0.7653 (tppt) REVERT: P 31 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8864 (tttp) REVERT: R 31 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.6763 (pttt) REVERT: R 90 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: R 105 LYS cc_start: 0.9146 (pptt) cc_final: 0.8881 (pttp) REVERT: S 59 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: T 92 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8406 (ptm160) REVERT: U 29 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.8109 (ttp80) REVERT: A 72 GLN cc_start: 0.8439 (tt0) cc_final: 0.8047 (tt0) REVERT: A 88 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7986 (mtm110) REVERT: A 160 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5815 (t80) REVERT: A 172 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 213 GLU cc_start: 0.7394 (tp30) cc_final: 0.6924 (tm-30) REVERT: A 259 MET cc_start: 0.8133 (mmp) cc_final: 0.7895 (mmm) REVERT: A 270 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 353 LEU cc_start: 0.8637 (tp) cc_final: 0.8386 (tt) REVERT: A 420 TYR cc_start: 0.7925 (t80) cc_final: 0.7672 (t80) REVERT: B 704 GLU cc_start: 0.8529 (pp20) cc_final: 0.8119 (pp20) REVERT: B 722 ASN cc_start: 0.8132 (m110) cc_final: 0.7857 (m-40) REVERT: B 775 TRP cc_start: 0.7928 (m100) cc_final: 0.7579 (m100) REVERT: B 809 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7689 (ptpt) REVERT: B 918 GLU cc_start: 0.8080 (tt0) cc_final: 0.7750 (tt0) REVERT: B 931 LEU cc_start: 0.8823 (mp) cc_final: 0.8600 (mt) REVERT: B 1164 MET cc_start: 0.7979 (ppp) cc_final: 0.7532 (ppp) REVERT: B 1194 MET cc_start: 0.7422 (pmm) cc_final: 0.6953 (pmm) REVERT: B 1223 TRP cc_start: 0.8123 (m-90) cc_final: 0.7653 (m100) REVERT: B 1257 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5352 (tpp) REVERT: E 316 MET cc_start: 0.6034 (pmm) cc_final: 0.5172 (tpt) REVERT: G 560 MET cc_start: 0.6711 (tmm) cc_final: 0.6162 (mtm) outliers start: 75 outliers final: 56 residues processed: 355 average time/residue: 0.4208 time to fit residues: 230.7524 Evaluate side-chains 373 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 302 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 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 241 LYS 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 354 LEU Chi-restraints excluded: chain O residue 48 LEU 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 59 GLU 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 52 ILE Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 160 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 246 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 270 GLN 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 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 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 540 THR 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: 3.9990 chunk 113 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 267 optimal weight: 6.9990 chunk 109 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 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 393 GLN ** 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 = 0.4170 r_free = 0.4170 target = 0.126330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087401 restraints weight = 67697.129| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.23 r_work: 0.3262 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28199 Z= 0.198 Angle : 0.629 12.082 39455 Z= 0.340 Chirality : 0.040 0.268 4355 Planarity : 0.004 0.094 3868 Dihedral : 27.096 176.085 6306 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.44 % Allowed : 28.36 % 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: -0.21 (0.17), residues: 2433 helix: 0.83 (0.14), residues: 1343 sheet: -1.88 (0.48), residues: 103 loop : -1.27 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 916 HIS 0.009 0.001 HIS B 785 PHE 0.037 0.002 PHE B1017 TYR 0.029 0.002 TYR A 211 ARG 0.009 0.000 ARG R 83 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1332) hydrogen bonds : angle 3.67402 ( 3564) metal coordination : bond 0.00139 ( 1) SS BOND : bond 0.00509 ( 1) SS BOND : angle 2.31179 ( 2) covalent geometry : bond 0.00449 (28197) covalent geometry : angle 0.62919 (39453) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21881.52 seconds wall clock time: 378 minutes 1.26 seconds (22681.26 seconds total)