Starting phenix.real_space_refine on Mon Aug 25 09:54:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd3_37123/08_2025/8kd3_37123.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 328 5.49 5 S 100 5.16 5 C 16471 2.51 5 N 4897 2.21 5 O 5779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27576 Number of models: 1 Model: "" Number of chains: 17 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: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4545 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 12, 'TRANS': 529} Chain breaks: 2 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 222} Chain breaks: 2 Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2620 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 3 Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1647 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 2 Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1043 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain breaks: 2 Chain: "O" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} 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: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, '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: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 848 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.20 Number of scatterers: 27576 At special positions: 0 Unit cell: (137.03, 161.17, 188.15, 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 100 16.00 P 328 15.00 O 5779 8.00 N 4897 7.00 C 16471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS G 263 " - pdb=" SG CYS G 266 " distance=2.03 Simple disulfide: pdb=" SG CYS G 303 " - pdb=" SG CYS G 306 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 748.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 188 " 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4866 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 18 sheets defined 56.7% alpha, 3.6% beta 139 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.295A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.933A pdb=" N LYS A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 61 " --> pdb=" O TYR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 115 through 136 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.574A pdb=" N LEU A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.838A 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 287 through 300 removed outlier: 4.011A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 removed outlier: 3.564A pdb=" N ARG A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.569A pdb=" N TYR A 346 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 347 " --> pdb=" O TYR A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'B' and resid 665 through 677 removed outlier: 4.618A pdb=" N PHE B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 Processing helix chain 'B' and resid 698 through 710 removed outlier: 3.550A 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 759 through 764 removed outlier: 3.674A pdb=" N THR B 763 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 764 " --> pdb=" O LYS B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 764' Processing helix chain 'B' and resid 771 through 778 Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.711A pdb=" N ALA B 789 " --> pdb=" O HIS B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 839 removed outlier: 3.667A pdb=" N TYR B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.023A 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: 3.963A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 3.996A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 removed outlier: 4.035A pdb=" N LYS B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 967 removed outlier: 3.808A pdb=" N ILE B 955 " --> pdb=" O GLU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 4.085A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.632A pdb=" N ILE B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B1022 " --> pdb=" O ILE B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1164 removed outlier: 3.916A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.867A pdb=" N LYS B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1184 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1221 through 1230 Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.803A pdb=" N LEU B1239 " --> pdb=" O ALA B1236 " (cutoff:3.500A) removed outlier: 3.748A 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: 3.863A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B1258 " --> pdb=" O HIS B1254 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1273 Processing helix chain 'B' and resid 1282 through 1294 Processing helix chain 'B' and resid 1307 through 1309 No H-bonds generated for 'chain 'B' and resid 1307 through 1309' 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: 3.587A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 293 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.517A pdb=" N ILE D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 344 removed outlier: 4.038A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 removed outlier: 3.503A pdb=" N HIS D 369 " --> pdb=" O TRP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'E' and resid 292 through 296 removed outlier: 3.905A 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 removed outlier: 3.712A pdb=" N ILE E 327 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 removed outlier: 4.118A pdb=" N LYS E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 360 removed outlier: 3.984A pdb=" N THR E 360 " --> pdb=" O TYR E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'E' and resid 402 through 407 removed outlier: 3.566A pdb=" N THR E 405 " --> pdb=" O ASN E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 543 through 559 Processing helix chain 'F' and resid 98 through 113 removed outlier: 3.808A pdb=" N GLU F 102 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 239 removed outlier: 3.972A pdb=" N VAL F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 238 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 removed outlier: 4.371A pdb=" N VAL F 257 " --> pdb=" O THR F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 275 through 292 removed outlier: 4.318A pdb=" N TYR F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 314 Processing helix chain 'F' and resid 328 through 338 removed outlier: 4.310A pdb=" N LEU F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 348 through 368 removed outlier: 3.709A pdb=" N CYS F 352 " --> pdb=" O ASP F 348 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET F 368 " --> pdb=" O VAL F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 321 through 329 removed outlier: 3.729A pdb=" N ASN G 325 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 328 " --> pdb=" O ASN G 325 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN G 329 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.828A pdb=" N PHE G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.999A 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 570 removed outlier: 3.568A pdb=" N GLN G 570 " --> pdb=" O LEU G 566 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.680A pdb=" N LYS O 56 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.538A pdb=" N PHE O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 25 through 29 removed outlier: 3.756A 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: 3.929A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 92 removed outlier: 3.573A 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 74 removed outlier: 4.346A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.581A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 119 Processing helix chain 'S' and resid 44 through 56 removed outlier: 3.582A pdb=" N LYS S 56 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.757A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 24 through 29 removed outlier: 3.794A pdb=" N GLN T 27 " --> pdb=" O ASP T 24 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.790A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 26 through 36 Processing helix chain 'U' and resid 45 through 73 removed outlier: 4.179A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.561A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 removed outlier: 3.782A pdb=" N ASN V 81 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 99 removed outlier: 3.511A pdb=" N ILE V 91 " --> pdb=" O THR V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 119 removed outlier: 4.023A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.272A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY A 309 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASN A 144 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N GLY A 311 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY A 310 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS A 271 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL A 234 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 4.156A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 974 through 978 removed outlier: 5.070A pdb=" N LEU B 975 " --> pdb=" O ILE B1314 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B1314 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 977 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B1312 " --> pdb=" O PHE B 977 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA6, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA7, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA8, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.833A pdb=" N TYR E 505 " --> pdb=" O ILE E 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 521 through 522 removed outlier: 5.704A pdb=" N GLN E 521 " --> pdb=" O ILE E 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.905A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.212A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.399A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'S' and resid 83 through 84 removed outlier: 7.190A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.028A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'U' and resid 77 through 78 983 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 6.77 Time building geometry restraints manager: 2.55 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: 7213 1.34 - 1.46: 7823 1.46 - 1.58: 12964 1.58 - 1.70: 656 1.70 - 1.82: 153 Bond restraints: 28809 Sorted by residual: bond pdb=" CB PRO D 319 " pdb=" CG PRO D 319 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+01 bond pdb=" N ASP E 288 " pdb=" CA ASP E 288 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" N ILE E 395 " pdb=" CA ILE E 395 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.38e+00 bond pdb=" N ILE E 291 " pdb=" CA ILE E 291 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.93e+00 bond pdb=" N THR E 396 " pdb=" CA THR E 396 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.99e+00 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 40012 3.48 - 6.96: 222 6.96 - 10.44: 35 10.44 - 13.92: 9 13.92 - 17.40: 7 Bond angle restraints: 40285 Sorted by residual: angle pdb=" CA PRO D 319 " pdb=" N PRO D 319 " pdb=" CD PRO D 319 " ideal model delta sigma weight residual 112.00 97.32 14.68 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO B 853 " pdb=" N PRO B 853 " pdb=" CD PRO B 853 " ideal model delta sigma weight residual 112.00 102.60 9.40 1.40e+00 5.10e-01 4.51e+01 angle pdb=" CB MET D 107 " pdb=" CG MET D 107 " pdb=" SD MET D 107 " ideal model delta sigma weight residual 112.70 130.10 -17.40 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA MET D 107 " pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 114.10 125.29 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" CB MET O 90 " pdb=" CG MET O 90 " pdb=" SD MET O 90 " ideal model delta sigma weight residual 112.70 128.61 -15.91 3.00e+00 1.11e-01 2.81e+01 ... (remaining 40280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14402 35.15 - 70.29: 2026 70.29 - 105.44: 60 105.44 - 140.59: 2 140.59 - 175.74: 1 Dihedral angle restraints: 16491 sinusoidal: 8965 harmonic: 7526 Sorted by residual: dihedral pdb=" CB CYS G 263 " pdb=" SG CYS G 263 " pdb=" SG CYS G 266 " pdb=" CB CYS G 266 " ideal model delta sinusoidal sigma weight residual 93.00 46.45 46.55 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA GLU B1220 " pdb=" C GLU B1220 " pdb=" N HIS B1221 " pdb=" CA HIS B1221 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C MET D 107 " pdb=" N MET D 107 " pdb=" CA MET D 107 " pdb=" CB MET D 107 " ideal model delta harmonic sigma weight residual -122.60 -132.87 10.27 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4154 0.081 - 0.161: 267 0.161 - 0.242: 17 0.242 - 0.323: 3 0.323 - 0.403: 1 Chirality restraints: 4442 Sorted by residual: chirality pdb=" CA ILE E 395 " pdb=" N ILE E 395 " pdb=" C ILE E 395 " pdb=" CB ILE E 395 " both_signs ideal model delta sigma weight residual False 2.43 2.84 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CB ILE F 105 " pdb=" CA ILE F 105 " pdb=" CG1 ILE F 105 " pdb=" CG2 ILE F 105 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA MET D 107 " pdb=" N MET D 107 " pdb=" C MET D 107 " pdb=" CB MET D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4439 not shown) Planarity restraints: 3978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 852 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.02e+01 pdb=" N PRO B 853 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 853 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 853 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 318 " 0.073 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 319 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 88 " -0.023 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" CG TYR P 88 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR P 88 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR P 88 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR P 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 88 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR P 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR P 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 3975 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 5 2.01 - 2.73: 1570 2.73 - 3.45: 38270 3.45 - 4.18: 72964 4.18 - 4.90: 117351 Nonbonded interactions: 230160 Sorted by model distance: nonbonded pdb=" OE2 GLU B 885 " pdb=" CD2 HIS B 886 " model vdw 1.281 3.260 nonbonded pdb=" NE2 HIS O 113 " pdb=" OD1 ASP S 123 " model vdw 1.391 3.120 nonbonded pdb=" OD1 ASP B 872 " pdb=" O ILE E 54 " model vdw 1.709 3.040 nonbonded pdb=" CB ALA A 36 " pdb=" CD2 LEU E 48 " model vdw 1.813 3.880 nonbonded pdb=" OE2 GLU B 816 " pdb=" OD1 ASP E 47 " model vdw 1.850 3.040 ... (remaining 230155 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 113 or resid 222 through \ 373)) selection = chain 'F' } ncs_group { reference = (chain 'O' and resid 36 through 133) selection = (chain 'S' and resid 36 through 133) } ncs_group { reference = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } 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: 11.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.740 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 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 0.185 28814 Z= 0.204 Angle : 0.772 17.397 40291 Z= 0.425 Chirality : 0.043 0.403 4442 Planarity : 0.006 0.137 3978 Dihedral : 24.414 175.735 11616 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.13 % Allowed : 30.60 % Favored : 69.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.16), residues: 2507 helix: -0.20 (0.13), residues: 1350 sheet: 0.83 (0.61), residues: 93 loop : -1.83 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG U 71 TYR 0.066 0.001 TYR P 88 PHE 0.023 0.001 PHE B 985 TRP 0.046 0.001 TRP F 365 HIS 0.005 0.001 HIS R 46 Details of bonding type rmsd covalent geometry : bond 0.00389 (28809) covalent geometry : angle 0.77209 (40285) SS BOND : bond 0.00522 ( 3) SS BOND : angle 0.90434 ( 6) hydrogen bonds : bond 0.10934 ( 1350) hydrogen bonds : angle 4.89267 ( 3635) metal coordination : bond 0.00030 ( 1) Misc. bond : bond 0.06595 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 324 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.8387 (t) cc_final: 0.8034 (m) REVERT: D 107 MET cc_start: 0.7324 (ttt) cc_final: 0.7025 (mmp) REVERT: D 223 GLN cc_start: 0.6619 (pp30) cc_final: 0.6350 (pp30) REVERT: F 307 ASP cc_start: 0.4858 (t70) cc_final: 0.4589 (t70) REVERT: F 340 GLU cc_start: 0.4745 (pm20) cc_final: 0.4526 (tm-30) outliers start: 3 outliers final: 0 residues processed: 326 average time/residue: 0.5494 time to fit residues: 212.8232 Evaluate side-chains 280 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS E 402 ASN E 517 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 HIS O 39 HIS P 25 ASN Q 38 ASN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN S 85 GLN S 93 GLN U 38 ASN V 60 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.137690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105548 restraints weight = 56665.388| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.01 r_work: 0.3375 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 28814 Z= 0.290 Angle : 0.661 11.716 40291 Z= 0.359 Chirality : 0.042 0.294 4442 Planarity : 0.005 0.067 3978 Dihedral : 26.503 176.309 6379 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.58 % Allowed : 24.14 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.16), residues: 2507 helix: 0.25 (0.13), residues: 1385 sheet: 0.41 (0.59), residues: 94 loop : -1.61 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG U 71 TYR 0.024 0.002 TYR A 347 PHE 0.019 0.002 PHE B 720 TRP 0.018 0.002 TRP F 365 HIS 0.020 0.002 HIS B 886 Details of bonding type rmsd covalent geometry : bond 0.00606 (28809) covalent geometry : angle 0.66062 (40285) SS BOND : bond 0.00694 ( 3) SS BOND : angle 2.33848 ( 6) hydrogen bonds : bond 0.04487 ( 1350) hydrogen bonds : angle 3.84043 ( 3635) metal coordination : bond 0.00300 ( 1) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 351 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6378 (p90) REVERT: A 204 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: A 298 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8052 (t) REVERT: A 373 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7091 (mpp) REVERT: B 985 PHE cc_start: 0.8447 (m-10) cc_final: 0.8215 (m-80) REVERT: D 357 LYS cc_start: 0.8258 (tptt) cc_final: 0.7980 (ttmt) REVERT: D 368 MET cc_start: 0.6956 (mmm) cc_final: 0.6661 (mmp) REVERT: E 387 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6096 (t80) REVERT: E 435 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7621 (mmt90) REVERT: E 556 TYR cc_start: 0.8496 (m-10) cc_final: 0.8277 (m-10) REVERT: F 22 MET cc_start: 0.0768 (OUTLIER) cc_final: 0.0431 (mtp) REVERT: F 244 LYS cc_start: 0.1368 (OUTLIER) cc_final: 0.0590 (tptt) REVERT: F 368 MET cc_start: 0.4071 (OUTLIER) cc_final: 0.3184 (ppp) REVERT: P 40 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8967 (ttm170) REVERT: P 44 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8441 (tmtt) REVERT: Q 90 ASP cc_start: 0.8377 (t0) cc_final: 0.8117 (t70) REVERT: R 45 VAL cc_start: 0.8794 (p) cc_final: 0.8527 (m) REVERT: R 73 GLU cc_start: 0.8527 (tp30) cc_final: 0.8171 (tp30) REVERT: T 27 GLN cc_start: 0.8751 (mm110) cc_final: 0.8525 (tp40) outliers start: 127 outliers final: 35 residues processed: 432 average time/residue: 0.7583 time to fit residues: 379.0671 Evaluate side-chains 346 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 717 PHE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1214 LEU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 22 MET Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 244 LYS Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain P residue 40 ARG Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 121 optimal weight: 0.0570 chunk 203 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 210 optimal weight: 0.5980 chunk 229 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 330 ASN B 886 HIS D 393 GLN F 317 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 104 GLN V 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.138436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106319 restraints weight = 57147.895| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.99 r_work: 0.3396 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28814 Z= 0.138 Angle : 0.557 11.562 40291 Z= 0.302 Chirality : 0.036 0.168 4442 Planarity : 0.004 0.055 3978 Dihedral : 26.506 173.695 6379 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.21 % Allowed : 25.86 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2507 helix: 0.77 (0.14), residues: 1381 sheet: 0.06 (0.58), residues: 94 loop : -1.47 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 324 TYR 0.018 0.001 TYR A 347 PHE 0.012 0.001 PHE B 669 TRP 0.013 0.001 TRP B 775 HIS 0.012 0.001 HIS B 886 Details of bonding type rmsd covalent geometry : bond 0.00300 (28809) covalent geometry : angle 0.55594 (40285) SS BOND : bond 0.00695 ( 3) SS BOND : angle 2.26201 ( 6) hydrogen bonds : bond 0.03369 ( 1350) hydrogen bonds : angle 3.62331 ( 3635) metal coordination : bond 0.00157 ( 1) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 326 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7346 (t) REVERT: A 248 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7920 (mmm-85) REVERT: D 82 GLN cc_start: 0.7223 (pm20) cc_final: 0.6827 (mm110) REVERT: D 311 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7652 (mtpp) REVERT: D 317 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7352 (mm110) REVERT: D 357 LYS cc_start: 0.8245 (tptt) cc_final: 0.7971 (ttmt) REVERT: D 368 MET cc_start: 0.7199 (mmm) cc_final: 0.6876 (mmp) REVERT: E 387 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6123 (t80) REVERT: E 435 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7972 (mmt90) REVERT: E 548 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7751 (ptpp) REVERT: F 96 ARG cc_start: 0.0457 (OUTLIER) cc_final: -0.0976 (mmt180) REVERT: F 107 MET cc_start: 0.0043 (OUTLIER) cc_final: -0.0519 (ptt) REVERT: F 237 GLU cc_start: 0.4507 (tp30) cc_final: 0.3359 (pm20) REVERT: O 131 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8902 (mtt-85) REVERT: P 44 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8327 (tmtt) REVERT: P 50 ILE cc_start: 0.8866 (tt) cc_final: 0.8589 (tt) REVERT: Q 51 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8876 (tp) REVERT: Q 73 ASN cc_start: 0.8643 (t0) cc_final: 0.8435 (t0) REVERT: Q 90 ASP cc_start: 0.8326 (t0) cc_final: 0.8036 (t70) REVERT: R 45 VAL cc_start: 0.8816 (p) cc_final: 0.8578 (m) REVERT: R 53 SER cc_start: 0.9236 (p) cc_final: 0.8857 (m) REVERT: T 91 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8494 (tttt) REVERT: V 76 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8145 (mtt180) outliers start: 96 outliers final: 29 residues processed: 384 average time/residue: 0.6886 time to fit residues: 307.2644 Evaluate side-chains 341 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 365 LYS Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 81 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 175 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN R 60 ASN S 55 GLN ** S 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 25 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098393 restraints weight = 55745.460| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.97 r_work: 0.3231 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28814 Z= 0.198 Angle : 0.603 11.507 40291 Z= 0.328 Chirality : 0.039 0.236 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.549 176.167 6379 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.31 % Allowed : 24.06 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.16), residues: 2507 helix: 0.76 (0.14), residues: 1388 sheet: -0.46 (0.55), residues: 93 loop : -1.38 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 83 TYR 0.023 0.002 TYR A 347 PHE 0.016 0.001 PHE B 669 TRP 0.021 0.002 TRP B 719 HIS 0.006 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00443 (28809) covalent geometry : angle 0.60279 (40285) SS BOND : bond 0.00614 ( 3) SS BOND : angle 2.11027 ( 6) hydrogen bonds : bond 0.03885 ( 1350) hydrogen bonds : angle 3.65187 ( 3635) metal coordination : bond 0.00193 ( 1) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 329 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.6985 (p90) REVERT: A 211 TYR cc_start: 0.8073 (t80) cc_final: 0.7763 (t80) REVERT: A 248 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8152 (mmm-85) REVERT: A 313 TYR cc_start: 0.7303 (m-80) cc_final: 0.6943 (m-80) REVERT: B 695 ASP cc_start: 0.7892 (m-30) cc_final: 0.7676 (m-30) REVERT: B 701 ASP cc_start: 0.7504 (m-30) cc_final: 0.7294 (m-30) REVERT: B 822 GLU cc_start: 0.6783 (pt0) cc_final: 0.6253 (pt0) REVERT: B 986 TYR cc_start: 0.8002 (m-10) cc_final: 0.7787 (m-10) REVERT: B 1006 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (t70) REVERT: B 1182 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7201 (mppt) REVERT: D 82 GLN cc_start: 0.7248 (pm20) cc_final: 0.6960 (mm110) REVERT: D 311 LYS cc_start: 0.8142 (mmpt) cc_final: 0.7776 (mtpp) REVERT: D 393 GLN cc_start: 0.8705 (mp-120) cc_final: 0.8477 (mm-40) REVERT: E 333 VAL cc_start: 0.5899 (m) cc_final: 0.5678 (p) REVERT: E 350 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8986 (tt0) REVERT: E 371 GLN cc_start: 0.8682 (pm20) cc_final: 0.8237 (pm20) REVERT: E 540 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7535 (p) REVERT: E 548 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7310 (ptpt) REVERT: F 96 ARG cc_start: 0.0681 (OUTLIER) cc_final: -0.0813 (mmt180) REVERT: F 107 MET cc_start: 0.0096 (OUTLIER) cc_final: -0.0357 (ptt) REVERT: F 241 LYS cc_start: 0.2341 (OUTLIER) cc_final: 0.1986 (mmmt) REVERT: F 368 MET cc_start: 0.4399 (ppp) cc_final: 0.2825 (tpt) REVERT: G 332 ASN cc_start: 0.4522 (m-40) cc_final: 0.3427 (p0) REVERT: P 44 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8390 (tmtt) REVERT: Q 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8533 (t0) REVERT: Q 90 ASP cc_start: 0.8321 (t0) cc_final: 0.8025 (t70) REVERT: R 53 SER cc_start: 0.9192 (p) cc_final: 0.8883 (m) outliers start: 121 outliers final: 42 residues processed: 414 average time/residue: 0.6894 time to fit residues: 329.5395 Evaluate side-chains 347 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 44 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 239 optimal weight: 0.0980 chunk 230 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Q 104 GLN R 60 ASN V 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100323 restraints weight = 55737.276| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.79 r_work: 0.3281 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28814 Z= 0.147 Angle : 0.563 12.657 40291 Z= 0.306 Chirality : 0.037 0.171 4442 Planarity : 0.004 0.067 3978 Dihedral : 26.503 173.649 6379 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.21 % Allowed : 25.59 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.17), residues: 2507 helix: 0.92 (0.14), residues: 1394 sheet: -0.68 (0.54), residues: 93 loop : -1.34 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 324 TYR 0.017 0.001 TYR A 347 PHE 0.015 0.001 PHE A 160 TRP 0.021 0.001 TRP E 301 HIS 0.004 0.001 HIS R 46 Details of bonding type rmsd covalent geometry : bond 0.00325 (28809) covalent geometry : angle 0.56263 (40285) SS BOND : bond 0.00655 ( 3) SS BOND : angle 2.14219 ( 6) hydrogen bonds : bond 0.03288 ( 1350) hydrogen bonds : angle 3.55586 ( 3635) metal coordination : bond 0.00179 ( 1) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 308 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6744 (p90) REVERT: A 248 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8078 (mmm-85) REVERT: A 313 TYR cc_start: 0.7128 (m-80) cc_final: 0.6833 (m-80) REVERT: A 380 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8927 (mp) REVERT: B 695 ASP cc_start: 0.7903 (m-30) cc_final: 0.7686 (m-30) REVERT: B 821 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 878 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: B 986 TYR cc_start: 0.7948 (m-10) cc_final: 0.7693 (m-10) REVERT: B 1006 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8112 (t70) REVERT: D 82 GLN cc_start: 0.7348 (pm20) cc_final: 0.7102 (mm110) REVERT: D 107 MET cc_start: 0.7380 (pmm) cc_final: 0.6847 (pp-130) REVERT: D 311 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7819 (mtpp) REVERT: E 41 SER cc_start: 0.4701 (OUTLIER) cc_final: 0.4412 (p) REVERT: E 350 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8918 (tt0) REVERT: E 371 GLN cc_start: 0.8622 (pm20) cc_final: 0.8190 (pm20) REVERT: E 548 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7383 (ptpt) REVERT: F 96 ARG cc_start: 0.0697 (OUTLIER) cc_final: -0.0787 (mmt180) REVERT: F 107 MET cc_start: 0.0052 (OUTLIER) cc_final: -0.0395 (ptt) REVERT: F 235 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5762 (t0) REVERT: F 241 LYS cc_start: 0.2319 (OUTLIER) cc_final: 0.1964 (mmmt) REVERT: G 332 ASN cc_start: 0.4505 (m-40) cc_final: 0.3408 (p0) REVERT: G 556 TYR cc_start: 0.5792 (OUTLIER) cc_final: 0.4911 (m-80) REVERT: P 50 ILE cc_start: 0.8797 (tt) cc_final: 0.8454 (tt) REVERT: Q 73 ASN cc_start: 0.8835 (t0) cc_final: 0.8543 (t0) REVERT: Q 90 ASP cc_start: 0.8253 (t0) cc_final: 0.7981 (t70) REVERT: R 53 SER cc_start: 0.9144 (p) cc_final: 0.8880 (m) REVERT: R 90 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: U 75 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8936 (mttm) outliers start: 96 outliers final: 35 residues processed: 375 average time/residue: 0.6720 time to fit residues: 292.6021 Evaluate side-chains 341 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 878 GLU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1006 ASP Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1230 GLN Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 308 PHE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 556 TYR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 157 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 72 optimal weight: 0.0570 chunk 67 optimal weight: 0.0270 chunk 44 optimal weight: 8.9990 chunk 241 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 271 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN D 393 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.131986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100560 restraints weight = 55848.965| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.74 r_work: 0.3282 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28814 Z= 0.148 Angle : 0.561 13.106 40291 Z= 0.306 Chirality : 0.037 0.181 4442 Planarity : 0.004 0.052 3978 Dihedral : 26.429 174.754 6379 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.69 % Allowed : 26.29 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.17), residues: 2507 helix: 1.05 (0.14), residues: 1393 sheet: -0.75 (0.54), residues: 93 loop : -1.35 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 83 TYR 0.031 0.001 TYR P 88 PHE 0.016 0.001 PHE A 160 TRP 0.024 0.001 TRP E 301 HIS 0.005 0.001 HIS B 785 Details of bonding type rmsd covalent geometry : bond 0.00329 (28809) covalent geometry : angle 0.56087 (40285) SS BOND : bond 0.00650 ( 3) SS BOND : angle 2.11428 ( 6) hydrogen bonds : bond 0.03286 ( 1350) hydrogen bonds : angle 3.49585 ( 3635) metal coordination : bond 0.00169 ( 1) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 306 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.6827 (p90) REVERT: A 248 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (mtp-110) REVERT: A 313 TYR cc_start: 0.7156 (m-80) cc_final: 0.6859 (m-80) REVERT: A 380 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8931 (mp) REVERT: B 821 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8326 (mp) REVERT: D 107 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6838 (pp-130) REVERT: D 311 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7794 (mtpp) REVERT: E 41 SER cc_start: 0.4796 (OUTLIER) cc_final: 0.4484 (p) REVERT: E 350 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8939 (tt0) REVERT: E 371 GLN cc_start: 0.8631 (pm20) cc_final: 0.8201 (pm20) REVERT: E 548 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7379 (ptpt) REVERT: F 96 ARG cc_start: 0.0899 (OUTLIER) cc_final: -0.0814 (mmt180) REVERT: F 107 MET cc_start: -0.0003 (OUTLIER) cc_final: -0.0458 (ptt) REVERT: F 235 ASP cc_start: 0.5947 (OUTLIER) cc_final: 0.5716 (t0) REVERT: F 241 LYS cc_start: 0.2387 (OUTLIER) cc_final: 0.1995 (mmmt) REVERT: F 368 MET cc_start: 0.4304 (OUTLIER) cc_final: 0.1981 (tpt) REVERT: G 332 ASN cc_start: 0.4444 (m-40) cc_final: 0.3533 (p0) REVERT: P 50 ILE cc_start: 0.8791 (tt) cc_final: 0.8453 (tt) REVERT: Q 73 ASN cc_start: 0.8836 (t0) cc_final: 0.8521 (t0) REVERT: Q 90 ASP cc_start: 0.8248 (t0) cc_final: 0.7964 (t70) REVERT: R 53 SER cc_start: 0.9126 (p) cc_final: 0.8887 (m) REVERT: R 90 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: U 75 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8952 (mttm) outliers start: 84 outliers final: 36 residues processed: 363 average time/residue: 0.7304 time to fit residues: 308.6746 Evaluate side-chains 336 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 456 SER Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 241 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.130739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.098174 restraints weight = 55586.765| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.84 r_work: 0.3247 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28814 Z= 0.168 Angle : 0.574 12.374 40291 Z= 0.310 Chirality : 0.037 0.183 4442 Planarity : 0.004 0.078 3978 Dihedral : 26.426 174.494 6379 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.82 % Allowed : 26.25 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2507 helix: 1.06 (0.14), residues: 1388 sheet: -0.84 (0.54), residues: 93 loop : -1.30 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 83 TYR 0.035 0.001 TYR P 88 PHE 0.020 0.001 PHE A 160 TRP 0.024 0.001 TRP E 301 HIS 0.005 0.001 HIS B 785 Details of bonding type rmsd covalent geometry : bond 0.00375 (28809) covalent geometry : angle 0.57349 (40285) SS BOND : bond 0.00650 ( 3) SS BOND : angle 2.10935 ( 6) hydrogen bonds : bond 0.03363 ( 1350) hydrogen bonds : angle 3.49764 ( 3635) metal coordination : bond 0.00174 ( 1) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6096 (t80) REVERT: A 189 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6883 (p90) REVERT: A 313 TYR cc_start: 0.7318 (m-80) cc_final: 0.6960 (m-80) REVERT: A 380 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8907 (mp) REVERT: B 765 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.2752 (tpp) REVERT: B 821 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 1182 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7245 (mmtm) REVERT: B 1288 LEU cc_start: 0.8006 (mp) cc_final: 0.7738 (mm) REVERT: D 107 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6791 (pp-130) REVERT: D 311 LYS cc_start: 0.8161 (mmpt) cc_final: 0.7801 (mtpp) REVERT: E 41 SER cc_start: 0.5077 (OUTLIER) cc_final: 0.4798 (p) REVERT: E 350 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.9004 (tt0) REVERT: E 371 GLN cc_start: 0.8656 (pm20) cc_final: 0.8187 (pm20) REVERT: E 548 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7342 (ptpt) REVERT: F 96 ARG cc_start: 0.0830 (OUTLIER) cc_final: -0.0804 (mmt180) REVERT: F 107 MET cc_start: 0.0026 (OUTLIER) cc_final: -0.0444 (ptt) REVERT: F 235 ASP cc_start: 0.5995 (OUTLIER) cc_final: 0.5749 (t0) REVERT: F 241 LYS cc_start: 0.2349 (OUTLIER) cc_final: 0.1992 (mmmt) REVERT: F 368 MET cc_start: 0.4201 (OUTLIER) cc_final: 0.1867 (tpt) REVERT: G 313 ASN cc_start: 0.3788 (t0) cc_final: 0.3447 (m-40) REVERT: G 332 ASN cc_start: 0.4550 (m-40) cc_final: 0.3622 (p0) REVERT: P 50 ILE cc_start: 0.8808 (tt) cc_final: 0.8453 (tt) REVERT: Q 51 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8906 (tp) REVERT: Q 73 ASN cc_start: 0.8792 (t0) cc_final: 0.8477 (t0) REVERT: Q 90 ASP cc_start: 0.8270 (t0) cc_final: 0.7984 (t70) REVERT: R 53 SER cc_start: 0.9126 (p) cc_final: 0.8885 (m) REVERT: R 68 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7725 (tt0) REVERT: R 90 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: U 75 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8984 (mttm) outliers start: 87 outliers final: 39 residues processed: 363 average time/residue: 0.7049 time to fit residues: 299.3589 Evaluate side-chains 351 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 PHE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain E residue 548 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 119 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 121 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 798 HIS B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.130244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097696 restraints weight = 55783.226| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.86 r_work: 0.3236 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28814 Z= 0.167 Angle : 0.580 14.086 40291 Z= 0.313 Chirality : 0.037 0.168 4442 Planarity : 0.004 0.065 3978 Dihedral : 26.432 174.356 6379 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.51 % Allowed : 26.43 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2507 helix: 1.05 (0.14), residues: 1395 sheet: -0.92 (0.54), residues: 93 loop : -1.29 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 83 TYR 0.039 0.002 TYR P 88 PHE 0.018 0.001 PHE A 160 TRP 0.029 0.001 TRP E 301 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00371 (28809) covalent geometry : angle 0.57938 (40285) SS BOND : bond 0.00657 ( 3) SS BOND : angle 2.13150 ( 6) hydrogen bonds : bond 0.03366 ( 1350) hydrogen bonds : angle 3.50074 ( 3635) metal coordination : bond 0.00198 ( 1) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 305 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.6896 (p90) REVERT: A 313 TYR cc_start: 0.7398 (m-80) cc_final: 0.7086 (m-80) REVERT: A 380 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8934 (mp) REVERT: A 422 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.4551 (ttt-90) REVERT: B 765 MET cc_start: 0.3923 (OUTLIER) cc_final: 0.3145 (tpp) REVERT: B 821 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8336 (mp) REVERT: B 1182 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7084 (mppt) REVERT: B 1288 LEU cc_start: 0.8020 (mp) cc_final: 0.7749 (mm) REVERT: D 107 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6815 (pp-130) REVERT: D 311 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7795 (mtpp) REVERT: E 350 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9041 (tt0) REVERT: E 359 GLU cc_start: 0.7625 (pt0) cc_final: 0.7346 (pp20) REVERT: E 371 GLN cc_start: 0.8693 (pm20) cc_final: 0.8201 (pm20) REVERT: F 96 ARG cc_start: 0.0750 (OUTLIER) cc_final: -0.0830 (mmt180) REVERT: F 107 MET cc_start: 0.0045 (OUTLIER) cc_final: -0.0433 (ptt) REVERT: F 235 ASP cc_start: 0.6029 (OUTLIER) cc_final: 0.5769 (t0) REVERT: F 241 LYS cc_start: 0.2310 (OUTLIER) cc_final: 0.1973 (mmmt) REVERT: F 280 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6799 (tp30) REVERT: F 368 MET cc_start: 0.4162 (OUTLIER) cc_final: 0.1849 (tpt) REVERT: G 313 ASN cc_start: 0.3931 (t0) cc_final: 0.3602 (m-40) REVERT: G 332 ASN cc_start: 0.4579 (m-40) cc_final: 0.3372 (p0) REVERT: P 50 ILE cc_start: 0.8803 (tt) cc_final: 0.8450 (tt) REVERT: Q 51 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8933 (tp) REVERT: Q 73 ASN cc_start: 0.8771 (t0) cc_final: 0.8456 (t0) REVERT: Q 90 ASP cc_start: 0.8284 (t0) cc_final: 0.8006 (t70) REVERT: R 53 SER cc_start: 0.9113 (p) cc_final: 0.8879 (m) REVERT: R 90 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: S 94 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8132 (mm-30) outliers start: 80 outliers final: 41 residues processed: 359 average time/residue: 0.6736 time to fit residues: 282.7622 Evaluate side-chains 346 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 235 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 225 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.097373 restraints weight = 55838.246| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.94 r_work: 0.3229 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28814 Z= 0.155 Angle : 0.581 13.842 40291 Z= 0.313 Chirality : 0.037 0.163 4442 Planarity : 0.004 0.056 3978 Dihedral : 26.422 174.302 6379 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.25 % Allowed : 26.95 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2507 helix: 1.05 (0.14), residues: 1396 sheet: -0.90 (0.54), residues: 93 loop : -1.27 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 83 TYR 0.043 0.002 TYR P 88 PHE 0.022 0.001 PHE A 160 TRP 0.034 0.001 TRP E 301 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00347 (28809) covalent geometry : angle 0.58079 (40285) SS BOND : bond 0.00656 ( 3) SS BOND : angle 2.12676 ( 6) hydrogen bonds : bond 0.03310 ( 1350) hydrogen bonds : angle 3.50140 ( 3635) metal coordination : bond 0.00172 ( 1) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 300 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6883 (p90) REVERT: A 313 TYR cc_start: 0.7387 (m-80) cc_final: 0.7072 (m-80) REVERT: A 380 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8935 (mp) REVERT: B 765 MET cc_start: 0.3985 (OUTLIER) cc_final: 0.3390 (tpp) REVERT: B 821 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 975 LEU cc_start: 0.8310 (tt) cc_final: 0.8081 (tp) REVERT: B 1288 LEU cc_start: 0.8021 (mp) cc_final: 0.7782 (mp) REVERT: D 107 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6812 (pp-130) REVERT: D 311 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7796 (mtpp) REVERT: E 350 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.9046 (tt0) REVERT: E 359 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7373 (pp20) REVERT: E 371 GLN cc_start: 0.8714 (pm20) cc_final: 0.8188 (pm20) REVERT: F 96 ARG cc_start: 0.0579 (OUTLIER) cc_final: -0.0754 (mmt180) REVERT: F 107 MET cc_start: 0.0083 (OUTLIER) cc_final: -0.0395 (ptt) REVERT: F 235 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5778 (t0) REVERT: F 241 LYS cc_start: 0.2282 (OUTLIER) cc_final: 0.1969 (mmmt) REVERT: F 280 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6826 (tp30) REVERT: F 368 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.1734 (tpt) REVERT: G 313 ASN cc_start: 0.3894 (t0) cc_final: 0.3589 (m-40) REVERT: G 332 ASN cc_start: 0.4650 (m-40) cc_final: 0.3480 (p0) REVERT: P 50 ILE cc_start: 0.8803 (tt) cc_final: 0.8447 (tt) REVERT: Q 51 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8938 (tp) REVERT: Q 73 ASN cc_start: 0.8757 (t0) cc_final: 0.8447 (t0) REVERT: R 53 SER cc_start: 0.9111 (p) cc_final: 0.8894 (m) REVERT: R 90 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7887 (mp0) outliers start: 74 outliers final: 45 residues processed: 350 average time/residue: 0.6155 time to fit residues: 252.8042 Evaluate side-chains 352 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 249 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 276 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.130093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096371 restraints weight = 55775.360| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.02 r_work: 0.3239 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28814 Z= 0.160 Angle : 0.589 13.619 40291 Z= 0.316 Chirality : 0.037 0.164 4442 Planarity : 0.004 0.054 3978 Dihedral : 26.416 174.379 6379 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.99 % Allowed : 27.13 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.17), residues: 2507 helix: 1.06 (0.14), residues: 1394 sheet: -0.94 (0.54), residues: 93 loop : -1.27 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 324 TYR 0.047 0.002 TYR P 88 PHE 0.021 0.001 PHE A 160 TRP 0.039 0.001 TRP E 301 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00358 (28809) covalent geometry : angle 0.58848 (40285) SS BOND : bond 0.00649 ( 3) SS BOND : angle 2.10563 ( 6) hydrogen bonds : bond 0.03323 ( 1350) hydrogen bonds : angle 3.49515 ( 3635) metal coordination : bond 0.00178 ( 1) Misc. bond : bond 0.00061 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5014 Ramachandran restraints generated. 2507 Oldfield, 0 Emsley, 2507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.6940 (p90) REVERT: A 313 TYR cc_start: 0.7530 (m-80) cc_final: 0.7079 (m-80) REVERT: A 380 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8967 (mp) REVERT: B 765 MET cc_start: 0.4279 (OUTLIER) cc_final: 0.3668 (tpp) REVERT: B 821 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (mp) REVERT: B 1182 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7129 (mppt) REVERT: B 1288 LEU cc_start: 0.8013 (mp) cc_final: 0.7786 (mp) REVERT: D 107 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6809 (pp-130) REVERT: D 311 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7805 (mtpp) REVERT: E 350 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9073 (tt0) REVERT: E 359 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7565 (pp20) REVERT: E 371 GLN cc_start: 0.8876 (pm20) cc_final: 0.8286 (pm20) REVERT: F 96 ARG cc_start: 0.0969 (OUTLIER) cc_final: -0.0786 (mmt180) REVERT: F 107 MET cc_start: 0.0085 (OUTLIER) cc_final: -0.0398 (ptt) REVERT: F 235 ASP cc_start: 0.6048 (OUTLIER) cc_final: 0.5774 (t0) REVERT: F 241 LYS cc_start: 0.2288 (OUTLIER) cc_final: 0.1975 (mmmt) REVERT: F 280 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6801 (tp30) REVERT: F 340 GLU cc_start: 0.7921 (pm20) cc_final: 0.7062 (tm-30) REVERT: F 368 MET cc_start: 0.4192 (OUTLIER) cc_final: 0.1748 (tpt) REVERT: G 313 ASN cc_start: 0.3925 (t0) cc_final: 0.3596 (m-40) REVERT: G 332 ASN cc_start: 0.4615 (m-40) cc_final: 0.3437 (p0) REVERT: P 50 ILE cc_start: 0.8908 (tt) cc_final: 0.8513 (tt) REVERT: Q 51 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8979 (tp) REVERT: Q 73 ASN cc_start: 0.8902 (t0) cc_final: 0.8566 (t0) REVERT: Q 90 ASP cc_start: 0.8573 (t0) cc_final: 0.8289 (t70) REVERT: R 53 SER cc_start: 0.9201 (p) cc_final: 0.8995 (m) REVERT: R 90 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: S 94 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 68 outliers final: 45 residues processed: 346 average time/residue: 0.6512 time to fit residues: 263.8416 Evaluate side-chains 350 residues out of total 2278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 765 MET Chi-restraints excluded: chain B residue 799 ARG Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 881 ASP Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 889 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 1159 LEU Chi-restraints excluded: chain B residue 1182 LYS Chi-restraints excluded: chain B residue 1308 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 511 LYS Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 107 MET Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 241 LYS Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain G residue 308 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 46 HIS Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 102 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 204 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 185 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1230 GLN ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN V 60 ASN V 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.130831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097617 restraints weight = 55766.889| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.94 r_work: 0.3254 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28814 Z= 0.141 Angle : 0.579 12.609 40291 Z= 0.312 Chirality : 0.037 0.162 4442 Planarity : 0.004 0.059 3978 Dihedral : 26.381 174.208 6379 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.68 % Allowed : 27.61 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2507 helix: 1.07 (0.14), residues: 1397 sheet: -0.96 (0.54), residues: 93 loop : -1.26 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 324 TYR 0.046 0.001 TYR P 88 PHE 0.019 0.001 PHE A 160 TRP 0.043 0.001 TRP E 301 HIS 0.005 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00311 (28809) covalent geometry : angle 0.57845 (40285) SS BOND : bond 0.00641 ( 3) SS BOND : angle 2.09361 ( 6) hydrogen bonds : bond 0.03188 ( 1350) hydrogen bonds : angle 3.47415 ( 3635) metal coordination : bond 0.00132 ( 1) Misc. bond : bond 0.00059 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11285.88 seconds wall clock time: 192 minutes 47.49 seconds (11567.49 seconds total)