Starting phenix.real_space_refine on Mon Oct 26 15:07:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0c_64661/10_2026/9v0c_64661.cif" } resolution = 3.27 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 125 5.16 5 C 13185 2.51 5 N 3560 2.21 5 O 3869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20745 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2897 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5717 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8682 Classifications: {'peptide': 1108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1067} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 660 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, '8W7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2125 SG CYS C 323 39.116 63.273 111.644 1.00201.35 S ATOM 2141 SG CYS C 326 37.229 65.842 109.583 1.00197.27 S ATOM 2635 SG CYS C 391 35.709 64.314 112.792 1.00205.05 S ATOM 2654 SG CYS C 394 36.316 62.430 109.209 1.00202.03 S ATOM 18695 SG CYS I 176 32.872 34.180 99.160 1.00296.54 S ATOM 18719 SG CYS I 179 31.011 36.536 96.778 1.00292.86 S ATOM 18490 SG CYS I 148 31.323 49.248 114.137 1.00203.33 S ATOM 18513 SG CYS I 151 33.076 52.293 116.214 1.00225.78 S ATOM 19666 SG CYS R 42 29.982 33.746 75.326 1.00223.24 S ATOM 19685 SG CYS R 45 33.526 33.564 74.183 1.00223.37 S ATOM 19933 SG CYS R 83 32.513 31.698 77.419 1.00233.06 S ATOM 19862 SG CYS R 75 16.936 34.507 80.955 1.00261.32 S ATOM 20029 SG CYS R 94 21.055 35.321 80.699 1.00220.32 S ATOM 19752 SG CYS R 53 35.770 28.920 75.859 1.00275.55 S ATOM 19775 SG CYS R 56 36.862 25.212 75.319 1.00283.42 S ATOM 19812 SG CYS R 68 33.564 26.450 73.806 1.00261.95 S Time building chain proxies: 4.40, per 1000 atoms: 0.21 Number of scatterers: 20745 At special positions: 0 Unit cell: (163.086, 139.788, 162.027, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 125 16.00 O 3869 8.00 N 3560 7.00 C 13185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 721.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 326 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 323 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 394 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 391 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 192 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 196 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 179 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 176 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 164 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 168 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 148 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 151 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 16 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 40 sheets defined 31.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.643A pdb=" N VAL C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.042A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 233 through 238 removed outlier: 3.867A pdb=" N ASN C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 4.039A pdb=" N TYR C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 removed outlier: 3.890A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.685A pdb=" N ILE C 301 " --> pdb=" O GLN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'A' and resid 57 through 75 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.535A pdb=" N HIS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.103A pdb=" N GLU A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.561A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.547A pdb=" N GLY A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 226 through 252 removed outlier: 3.992A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.509A pdb=" N TYR A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.589A pdb=" N LEU A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.537A pdb=" N ILE A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.042A pdb=" N ARG A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.613A pdb=" N ALA A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.512A pdb=" N ASP A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 359' Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.520A pdb=" N GLU A 407 " --> pdb=" O ASN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.845A pdb=" N PHE A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 483 Processing helix chain 'A' and resid 488 through 513 removed outlier: 3.692A pdb=" N GLY A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 562 removed outlier: 3.587A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 620 through 633 Processing helix chain 'A' and resid 693 through 708 removed outlier: 3.928A pdb=" N ASP A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 722 removed outlier: 3.856A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.659A pdb=" N LYS B 254 " --> pdb=" O PRO B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.625A pdb=" N ARG B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 370 " --> pdb=" O LEU B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 986 through 990 removed outlier: 4.167A pdb=" N ARG B 989 " --> pdb=" O ASP B 986 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 990 " --> pdb=" O GLU B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 986 through 990' Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1097 through 1100 removed outlier: 3.811A pdb=" N ILE B1100 " --> pdb=" O PHE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1097 through 1100' Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.618A pdb=" N LEU B1129 " --> pdb=" O THR B1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.788A pdb=" N CYS D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 131 through 145 Processing helix chain 'I' and resid 157 through 167 removed outlier: 3.526A pdb=" N LEU I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 197 removed outlier: 3.687A pdb=" N LEU I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR I 190 " --> pdb=" O ARG I 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.035A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 91 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.724A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 80 removed outlier: 3.852A pdb=" N GLN C 163 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 101 removed outlier: 3.767A pdb=" N ALA C 159 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AA4, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AA5, first strand: chain 'C' and resid 359 through 362 Processing sheet with id=AA6, first strand: chain 'C' and resid 368 through 370 removed outlier: 4.117A pdb=" N ALA C 389 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY C 399 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N CYS C 391 " --> pdb=" O HIS C 397 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS C 397 " --> pdb=" O CYS C 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 589 through 592 removed outlier: 4.344A pdb=" N LYS R 26 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 639 through 642 Processing sheet with id=AB1, first strand: chain 'A' and resid 745 through 747 Processing sheet with id=AB2, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 4.519A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY B1026 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER B1042 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B1030 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 6 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.572A pdb=" N GLY B 21 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.945A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.925A pdb=" N ILE B 121 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.645A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 182 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 196 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.645A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 182 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 190 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.547A pdb=" N MET B 218 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 258 through 263 removed outlier: 4.033A pdb=" N CYS B 260 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 280 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 299 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.032A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 359 through 365 removed outlier: 3.954A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 365 removed outlier: 3.954A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 396 through 403 removed outlier: 5.541A pdb=" N GLU B 398 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 703 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 400 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 410 through 413 removed outlier: 4.534A pdb=" N VAL B 435 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.796A pdb=" N ILE B 471 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS B 460 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 469 " --> pdb=" O CYS B 460 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 462 " --> pdb=" O GLN B 467 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN B 467 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N SER B 480 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU B 486 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 500 through 503 removed outlier: 7.123A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 542 removed outlier: 4.229A pdb=" N CYS B 540 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 542 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 557 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER B 565 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 578 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS B 570 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 576 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 588 through 595 removed outlier: 4.506A pdb=" N SER B 590 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N HIS B 600 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 627 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY B 615 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 625 " --> pdb=" O GLY B 615 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 637 through 643 removed outlier: 3.540A pdb=" N VAL B 637 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.451A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B 737 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.713A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 819 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 847 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 848 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 850 " --> pdb=" O ALA B 862 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 862 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER B 854 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AD5, first strand: chain 'B' and resid 890 through 893 removed outlier: 6.943A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.597A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 930 " --> pdb=" O ARG B 947 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG B 947 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 932 " --> pdb=" O ILE B 945 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 941 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 957 through 961 removed outlier: 6.724A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 974 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU B 997 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 976 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 978 " --> pdb=" O GLN B 993 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 993 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1076 through 1077 Processing sheet with id=AD9, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.667A pdb=" N ALA D 35 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 146 through 147 removed outlier: 4.060A pdb=" N PHE I 146 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 175 removed outlier: 4.472A pdb=" N PHE I 174 " --> pdb=" O THR I 183 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 12 through 16 Processing sheet with id=AE4, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.539A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5534 1.33 - 1.45: 3535 1.45 - 1.57: 11896 1.57 - 1.70: 0 1.70 - 1.82: 187 Bond restraints: 21152 Sorted by residual: bond pdb=" C LEU A 54 " pdb=" N PRO A 55 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.20e-02 6.94e+03 2.34e+00 bond pdb=" C3 8W7 C 502 " pdb=" O4 8W7 C 502 " ideal model delta sigma weight residual 1.343 1.371 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" CA ASP B 243 " pdb=" CB ASP B 243 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.24e-01 bond pdb=" C GLY B 409 " pdb=" O GLY B 409 " ideal model delta sigma weight residual 1.233 1.225 0.008 8.80e-03 1.29e+04 8.08e-01 bond pdb=" N THR C 332 " pdb=" CA THR C 332 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.53e-01 ... (remaining 21147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 27806 1.39 - 2.77: 668 2.77 - 4.16: 109 4.16 - 5.55: 23 5.55 - 6.93: 6 Bond angle restraints: 28612 Sorted by residual: angle pdb=" N VAL B 52 " pdb=" CA VAL B 52 " pdb=" C VAL B 52 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.12e+01 angle pdb=" C HIS I 168 " pdb=" N THR I 169 " pdb=" CA THR I 169 " ideal model delta sigma weight residual 121.76 128.00 -6.24 2.19e+00 2.09e-01 8.11e+00 angle pdb=" C ARG A 742 " pdb=" N ASP A 743 " pdb=" CA ASP A 743 " ideal model delta sigma weight residual 122.46 126.45 -3.99 1.41e+00 5.03e-01 8.03e+00 angle pdb=" C PRO A 402 " pdb=" N ASN A 403 " pdb=" CA ASN A 403 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" N LYS B 769 " pdb=" CA LYS B 769 " pdb=" C LYS B 769 " ideal model delta sigma weight residual 113.18 109.69 3.49 1.33e+00 5.65e-01 6.87e+00 ... (remaining 28607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 12572 35.73 - 71.46: 227 71.46 - 107.19: 25 107.19 - 142.92: 1 142.92 - 178.65: 1 Dihedral angle restraints: 12826 sinusoidal: 5217 harmonic: 7609 Sorted by residual: dihedral pdb=" CB CYS B 18 " pdb=" SG CYS B 18 " pdb=" SG CYS B 313 " pdb=" CB CYS B 313 " ideal model delta sinusoidal sigma weight residual 93.00 154.67 -61.67 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CA GLY A 306 " pdb=" C GLY A 306 " pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG B1122 " pdb=" C ARG B1122 " pdb=" N GLU B1123 " pdb=" CA GLU B1123 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 12823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2400 0.039 - 0.079: 556 0.079 - 0.118: 245 0.118 - 0.158: 28 0.158 - 0.197: 1 Chirality restraints: 3230 Sorted by residual: chirality pdb=" CB VAL B1109 " pdb=" CA VAL B1109 " pdb=" CG1 VAL B1109 " pdb=" CG2 VAL B1109 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA THR C 332 " pdb=" N THR C 332 " pdb=" C THR C 332 " pdb=" CB THR C 332 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA VAL C 362 " pdb=" N VAL C 362 " pdb=" C VAL C 362 " pdb=" CB VAL C 362 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 3227 not shown) Planarity restraints: 3669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 8W7 C 502 " -0.158 2.00e-02 2.50e+03 1.77e-01 9.40e+02 pdb=" C2 8W7 C 502 " -0.090 2.00e-02 2.50e+03 pdb=" C3 8W7 C 502 " 0.027 2.00e-02 2.50e+03 pdb=" C4 8W7 C 502 " -0.109 2.00e-02 2.50e+03 pdb=" C5 8W7 C 502 " 0.006 2.00e-02 2.50e+03 pdb=" C6 8W7 C 502 " 0.075 2.00e-02 2.50e+03 pdb=" C7 8W7 C 502 " 0.194 2.00e-02 2.50e+03 pdb=" C8 8W7 C 502 " 0.099 2.00e-02 2.50e+03 pdb=" C9 8W7 C 502 " -0.407 2.00e-02 2.50e+03 pdb=" N1 8W7 C 502 " -0.049 2.00e-02 2.50e+03 pdb=" O1 8W7 C 502 " 0.316 2.00e-02 2.50e+03 pdb=" O4 8W7 C 502 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 141 " 0.020 2.00e-02 2.50e+03 1.72e-02 7.41e+00 pdb=" CG TRP D 141 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 141 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 141 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 141 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 141 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 8W7 C 502 " 0.007 2.00e-02 2.50e+03 1.99e-02 4.95e+00 pdb=" C12 8W7 C 502 " -0.001 2.00e-02 2.50e+03 pdb=" C13 8W7 C 502 " -0.023 2.00e-02 2.50e+03 pdb=" N2 8W7 C 502 " 0.034 2.00e-02 2.50e+03 pdb=" O3 8W7 C 502 " -0.016 2.00e-02 2.50e+03 ... (remaining 3666 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2516 2.75 - 3.29: 20029 3.29 - 3.83: 31719 3.83 - 4.36: 34989 4.36 - 4.90: 62642 Nonbonded interactions: 151895 Sorted by model distance: nonbonded pdb=" OE1 GLU B 213 " pdb=" OG SER B 236 " model vdw 2.218 3.040 nonbonded pdb=" NZ LYS R 26 " pdb=" O TRP R 27 " model vdw 2.230 3.120 nonbonded pdb=" OD1 ASP A 308 " pdb=" NE2 HIS A 339 " model vdw 2.231 3.120 nonbonded pdb=" O GLY A 634 " pdb=" NH1 ARG A 637 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLU U 51 " pdb=" OH TYR U 59 " model vdw 2.251 3.040 ... (remaining 151890 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.090 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.003 0.039 21176 Z= 0.126 Angle : 0.550 12.089 28630 Z= 0.285 Chirality : 0.041 0.197 3230 Planarity : 0.005 0.177 3669 Dihedral : 15.000 178.653 7891 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.52 (0.17), residues: 2584 helix: 1.86 (0.20), residues: 703 sheet: -0.60 (0.22), residues: 625 loop : -1.53 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 642 TYR 0.021 0.001 TYR C 355 PHE 0.019 0.001 PHE A 397 TRP 0.046 0.002 TRP D 141 HIS 0.005 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (21152) covalent geometry : angle 0.53693 / 0.28 (28612) SS BOND : bond 0.00357 / 0.19 ( 1) SS BOND : angle 0.92996 / 0.45 ( 2) hydrogen bonds : bond 0.21040 / 14.19 ( 842) hydrogen bonds : angle 7.32011 / 5.02 ( 2409) metal coordination : bond 0.01249 / 0.61 ( 23) metal coordination : angle 5.12075 / 3.37 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 PHE cc_start: 0.8212 (p90) cc_final: 0.7954 (p90) REVERT: C 125 TYR cc_start: 0.8690 (m-80) cc_final: 0.8403 (m-80) REVERT: C 140 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8391 (tm-30) REVERT: C 330 GLU cc_start: 0.8684 (mt-10) cc_final: 0.7654 (tm-30) REVERT: C 336 GLU cc_start: 0.8573 (pm20) cc_final: 0.8337 (pm20) REVERT: C 419 ARG cc_start: 0.8754 (tmm160) cc_final: 0.8485 (ttp-170) REVERT: A 91 GLU cc_start: 0.9111 (tt0) cc_final: 0.8786 (tp30) REVERT: A 110 CYS cc_start: 0.9589 (m) cc_final: 0.9354 (m) REVERT: A 176 GLU cc_start: 0.9447 (tt0) cc_final: 0.9191 (tm-30) REVERT: A 241 CYS cc_start: 0.9421 (t) cc_final: 0.9033 (p) REVERT: A 338 GLN cc_start: 0.9158 (mm110) cc_final: 0.8702 (pp30) REVERT: A 494 MET cc_start: 0.9123 (mmt) cc_final: 0.8306 (mmt) REVERT: A 528 LEU cc_start: 0.8592 (mt) cc_final: 0.8347 (mt) REVERT: A 569 TRP cc_start: 0.7761 (m100) cc_final: 0.7523 (m100) REVERT: A 601 MET cc_start: 0.7587 (ttp) cc_final: 0.7299 (ppp) REVERT: A 704 MET cc_start: 0.8659 (tpt) cc_final: 0.8394 (tpt) REVERT: A 713 ASN cc_start: 0.9340 (m-40) cc_final: 0.9043 (p0) REVERT: B 361 ASP cc_start: 0.9214 (t70) cc_final: 0.8909 (t0) REVERT: B 362 MET cc_start: 0.9480 (ptt) cc_final: 0.9227 (ptt) REVERT: B 437 MET cc_start: 0.9397 (ttp) cc_final: 0.9132 (tmm) REVERT: B 581 MET cc_start: 0.9175 (mmm) cc_final: 0.8816 (mmm) REVERT: B 947 ARG cc_start: 0.8961 (ptm160) cc_final: 0.8717 (ptm160) REVERT: B 1123 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8122 (tp30) REVERT: D 15 ARG cc_start: 0.9140 (ttm110) cc_final: 0.8801 (ttp-110) REVERT: D 46 GLN cc_start: 0.9456 (tt0) cc_final: 0.9211 (mt0) REVERT: D 74 TYR cc_start: 0.8490 (m-10) cc_final: 0.8124 (m-80) REVERT: N 9 THR cc_start: 0.9623 (m) cc_final: 0.9381 (p) REVERT: N 11 LYS cc_start: 0.9211 (mtpt) cc_final: 0.9010 (mtpt) REVERT: N 20 THR cc_start: 0.9498 (m) cc_final: 0.9193 (m) REVERT: N 40 GLN cc_start: 0.7275 (mt0) cc_final: 0.7068 (mt0) REVERT: N 44 ILE cc_start: 0.9377 (mt) cc_final: 0.9160 (mm) REVERT: N 51 ASN cc_start: 0.8977 (m-40) cc_final: 0.8738 (m-40) REVERT: N 52 ASP cc_start: 0.9279 (m-30) cc_final: 0.8881 (p0) REVERT: N 54 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8796 (mmtm) REVERT: R 54 ILE cc_start: 0.9386 (pt) cc_final: 0.9016 (pt) REVERT: R 55 GLU cc_start: 0.9543 (tp30) cc_final: 0.9034 (tm-30) REVERT: R 76 ASN cc_start: 0.9337 (t0) cc_final: 0.9089 (m-40) REVERT: R 81 PHE cc_start: 0.9186 (t80) cc_final: 0.8975 (t80) REVERT: R 89 LYS cc_start: 0.9574 (ttmm) cc_final: 0.9266 (mtmm) REVERT: U 3 ILE cc_start: 0.9327 (mt) cc_final: 0.8964 (tp) REVERT: U 15 LEU cc_start: 0.8706 (mt) cc_final: 0.8330 (mt) REVERT: U 21 ASP cc_start: 0.8924 (m-30) cc_final: 0.8266 (m-30) REVERT: U 34 GLU cc_start: 0.9107 (tp30) cc_final: 0.8440 (tm-30) REVERT: U 72 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7805 (ttm110) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1579 time to fit residues: 94.7292 Evaluate side-chains 235 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0070 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 ASN B 507 GLN B1113 GLN B1140 HIS R 48 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.088182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058153 restraints weight = 68123.544| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.45 r_work: 0.2895 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21176 Z= 0.135 Angle : 0.620 12.108 28630 Z= 0.317 Chirality : 0.043 0.211 3230 Planarity : 0.004 0.042 3669 Dihedral : 5.984 152.737 2830 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.14 % Allowed : 8.56 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.49 (0.17), residues: 2584 helix: 1.72 (0.20), residues: 725 sheet: -0.50 (0.21), residues: 640 loop : -1.52 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 742 TYR 0.016 0.001 TYR A 720 PHE 0.024 0.001 PHE A 397 TRP 0.030 0.001 TRP D 141 HIS 0.006 0.001 HIS B1140 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21152) covalent geometry : angle 0.60930 / 0.32 (28612) SS BOND : bond 0.00214 / 0.11 ( 1) SS BOND : angle 0.66585 / 0.30 ( 2) hydrogen bonds : bond 0.04405 / 3.05 ( 842) hydrogen bonds : angle 5.28899 / 3.64 ( 2409) metal coordination : bond 0.01003 / 0.51 ( 23) metal coordination : angle 4.96752 / 3.30 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8849 (m-80) cc_final: 0.8364 (m-80) REVERT: C 168 LEU cc_start: 0.8678 (mt) cc_final: 0.8385 (mp) REVERT: C 330 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7675 (tm-30) REVERT: C 337 ILE cc_start: 0.9178 (mt) cc_final: 0.8953 (mt) REVERT: A 88 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8880 (mp10) REVERT: A 110 CYS cc_start: 0.9663 (m) cc_final: 0.9427 (m) REVERT: A 176 GLU cc_start: 0.9495 (tt0) cc_final: 0.9247 (tm-30) REVERT: A 241 CYS cc_start: 0.9479 (t) cc_final: 0.9134 (p) REVERT: A 494 MET cc_start: 0.9019 (mmt) cc_final: 0.8526 (mmt) REVERT: A 533 TRP cc_start: 0.9242 (m100) cc_final: 0.8922 (m100) REVERT: A 569 TRP cc_start: 0.7857 (m100) cc_final: 0.7652 (m100) REVERT: A 704 MET cc_start: 0.8745 (tpt) cc_final: 0.8432 (tpt) REVERT: A 713 ASN cc_start: 0.9331 (m-40) cc_final: 0.9006 (p0) REVERT: A 720 TYR cc_start: 0.8834 (m-10) cc_final: 0.8629 (m-10) REVERT: B 282 MET cc_start: 0.9206 (tpp) cc_final: 0.8947 (tpp) REVERT: B 361 ASP cc_start: 0.9134 (t70) cc_final: 0.8797 (t0) REVERT: B 437 MET cc_start: 0.9387 (ttp) cc_final: 0.9121 (tmm) REVERT: B 553 SER cc_start: 0.8757 (m) cc_final: 0.8393 (p) REVERT: B 581 MET cc_start: 0.9170 (mmm) cc_final: 0.8922 (mmm) REVERT: B 875 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 939 GLU cc_start: 0.8055 (mp0) cc_final: 0.7638 (mp0) REVERT: B 969 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8485 (mm-30) REVERT: B 1105 MET cc_start: 0.9172 (mtm) cc_final: 0.8783 (mtm) REVERT: B 1123 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8154 (tp30) REVERT: D 15 ARG cc_start: 0.9168 (ttm110) cc_final: 0.8809 (ttp-110) REVERT: D 71 THR cc_start: 0.9626 (m) cc_final: 0.9149 (p) REVERT: D 74 TYR cc_start: 0.8835 (m-10) cc_final: 0.8317 (m-80) REVERT: D 78 ILE cc_start: 0.9079 (mm) cc_final: 0.8738 (mm) REVERT: N 12 GLU cc_start: 0.8829 (mp0) cc_final: 0.8595 (mp0) REVERT: N 31 GLU cc_start: 0.8920 (tp30) cc_final: 0.8526 (mm-30) REVERT: N 40 GLN cc_start: 0.7426 (mt0) cc_final: 0.7150 (mt0) REVERT: N 44 ILE cc_start: 0.9361 (mt) cc_final: 0.9131 (mm) REVERT: N 51 ASN cc_start: 0.8933 (m-40) cc_final: 0.8594 (m-40) REVERT: N 52 ASP cc_start: 0.9370 (m-30) cc_final: 0.8899 (p0) REVERT: N 54 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8817 (mmtm) REVERT: R 54 ILE cc_start: 0.9390 (pt) cc_final: 0.9126 (pt) REVERT: R 55 GLU cc_start: 0.9565 (tp30) cc_final: 0.9258 (pt0) REVERT: R 76 ASN cc_start: 0.9307 (t0) cc_final: 0.9095 (m-40) REVERT: R 81 PHE cc_start: 0.9185 (t80) cc_final: 0.8922 (t80) REVERT: R 89 LYS cc_start: 0.9623 (ttmm) cc_final: 0.9316 (mtmm) REVERT: U 18 GLU cc_start: 0.8503 (pm20) cc_final: 0.8192 (pm20) REVERT: U 21 ASP cc_start: 0.8914 (m-30) cc_final: 0.8350 (m-30) REVERT: U 27 LYS cc_start: 0.9575 (mmtm) cc_final: 0.9360 (tptt) REVERT: U 34 GLU cc_start: 0.9062 (tp30) cc_final: 0.8371 (tm-30) REVERT: U 59 TYR cc_start: 0.8991 (m-10) cc_final: 0.8656 (m-10) REVERT: U 72 ARG cc_start: 0.8629 (ttp80) cc_final: 0.7874 (ttm110) outliers start: 26 outliers final: 13 residues processed: 271 average time/residue: 0.1500 time to fit residues: 62.8252 Evaluate side-chains 240 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [55, 211, 14, 92, 246, 143, 169, 170, 201, 164, 75] chunk 55 optimal weight: 0.5980 chunk 211 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 333 GLN A 339 HIS B1113 GLN D 20 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058914 restraints weight = 67267.727| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 4.37 r_work: 0.2902 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21176 Z= 0.111 Angle : 0.555 10.067 28630 Z= 0.282 Chirality : 0.042 0.153 3230 Planarity : 0.003 0.043 3669 Dihedral : 5.922 151.591 2830 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.14 % Allowed : 10.72 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.41 (0.17), residues: 2584 helix: 1.82 (0.20), residues: 728 sheet: -0.43 (0.21), residues: 631 loop : -1.51 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 369 TYR 0.012 0.001 TYR C 363 PHE 0.022 0.001 PHE A 397 TRP 0.021 0.001 TRP D 141 HIS 0.005 0.001 HIS D 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (21152) covalent geometry : angle 0.54590 / 0.28 (28612) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.49268 / 0.22 ( 2) hydrogen bonds : bond 0.03826 / 2.66 ( 842) hydrogen bonds : angle 4.87835 / 3.36 ( 2409) metal coordination : bond 0.00823 / 0.43 ( 23) metal coordination : angle 4.19528 / 2.82 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 237 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8768 (m-80) cc_final: 0.8284 (t80) REVERT: C 168 LEU cc_start: 0.8714 (mt) cc_final: 0.8421 (mp) REVERT: C 330 GLU cc_start: 0.8632 (mt-10) cc_final: 0.7697 (tm-30) REVERT: C 337 ILE cc_start: 0.9171 (mt) cc_final: 0.8951 (mt) REVERT: A 88 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8878 (mp10) REVERT: A 110 CYS cc_start: 0.9646 (m) cc_final: 0.9390 (m) REVERT: A 146 MET cc_start: 0.9246 (tpp) cc_final: 0.9017 (tpp) REVERT: A 176 GLU cc_start: 0.9491 (tt0) cc_final: 0.9240 (tm-30) REVERT: A 241 CYS cc_start: 0.9473 (t) cc_final: 0.9118 (p) REVERT: A 482 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8317 (tp30) REVERT: A 494 MET cc_start: 0.9045 (mmt) cc_final: 0.8552 (mmt) REVERT: A 533 TRP cc_start: 0.9235 (m100) cc_final: 0.8973 (m100) REVERT: A 704 MET cc_start: 0.8757 (tpt) cc_final: 0.8374 (tpt) REVERT: A 713 ASN cc_start: 0.9337 (m-40) cc_final: 0.9037 (p0) REVERT: A 720 TYR cc_start: 0.8739 (m-10) cc_final: 0.8527 (m-10) REVERT: B 282 MET cc_start: 0.9160 (tpp) cc_final: 0.8883 (tpp) REVERT: B 361 ASP cc_start: 0.9133 (t70) cc_final: 0.8782 (t0) REVERT: B 437 MET cc_start: 0.9331 (ttp) cc_final: 0.9070 (tmm) REVERT: B 553 SER cc_start: 0.8668 (m) cc_final: 0.8339 (p) REVERT: B 581 MET cc_start: 0.9164 (mmm) cc_final: 0.8926 (mmm) REVERT: B 787 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 875 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 1123 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8059 (tp30) REVERT: D 15 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8810 (ttp-110) REVERT: D 63 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8846 (mtmt) REVERT: D 71 THR cc_start: 0.9617 (m) cc_final: 0.9119 (p) REVERT: D 74 TYR cc_start: 0.8887 (m-10) cc_final: 0.8241 (m-80) REVERT: D 78 ILE cc_start: 0.9054 (mm) cc_final: 0.8721 (mm) REVERT: N 4 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8314 (mtpp) REVERT: N 31 GLU cc_start: 0.8960 (tp30) cc_final: 0.8636 (mm-30) REVERT: N 40 GLN cc_start: 0.7396 (mt0) cc_final: 0.7093 (mt0) REVERT: N 44 ILE cc_start: 0.9291 (mt) cc_final: 0.9055 (mm) REVERT: N 52 ASP cc_start: 0.9410 (m-30) cc_final: 0.8826 (p0) REVERT: N 54 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8646 (mmmm) REVERT: R 47 ASN cc_start: 0.8437 (m-40) cc_final: 0.8188 (m-40) REVERT: R 54 ILE cc_start: 0.9416 (pt) cc_final: 0.9060 (pt) REVERT: R 55 GLU cc_start: 0.9568 (tp30) cc_final: 0.9277 (pt0) REVERT: R 76 ASN cc_start: 0.9264 (t0) cc_final: 0.9055 (m-40) REVERT: R 81 PHE cc_start: 0.9186 (t80) cc_final: 0.8920 (t80) REVERT: U 18 GLU cc_start: 0.8630 (pm20) cc_final: 0.8300 (pm20) REVERT: U 21 ASP cc_start: 0.9004 (m-30) cc_final: 0.8455 (m-30) REVERT: U 34 GLU cc_start: 0.9050 (tp30) cc_final: 0.8602 (tm-30) REVERT: U 59 TYR cc_start: 0.9088 (m-10) cc_final: 0.8695 (m-10) REVERT: U 72 ARG cc_start: 0.8666 (ttp80) cc_final: 0.7984 (ttm110) outliers start: 26 outliers final: 20 residues processed: 256 average time/residue: 0.1514 time to fit residues: 60.0847 Evaluate side-chains 235 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain U residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [251, 95, 223, 14, 185, 162, 253, 102, 134, 19, 27] chunk 251 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 223 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 708 GLN B 727 GLN B 805 HIS D 46 GLN N 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056712 restraints weight = 67838.738| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.37 r_work: 0.2864 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21176 Z= 0.179 Angle : 0.576 9.900 28630 Z= 0.296 Chirality : 0.042 0.160 3230 Planarity : 0.004 0.045 3669 Dihedral : 6.051 154.970 2830 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.98 % Allowed : 12.12 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.45 (0.17), residues: 2584 helix: 1.83 (0.20), residues: 729 sheet: -0.53 (0.20), residues: 646 loop : -1.54 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.017 0.001 TYR B 613 PHE 0.040 0.001 PHE C 150 TRP 0.032 0.002 TRP A 569 HIS 0.004 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (21152) covalent geometry : angle 0.56753 / 0.30 (28612) SS BOND : bond 0.00143 / 0.08 ( 1) SS BOND : angle 0.43564 / 0.20 ( 2) hydrogen bonds : bond 0.03943 / 2.73 ( 842) hydrogen bonds : angle 4.73983 / 3.29 ( 2409) metal coordination : bond 0.00777 / 0.43 ( 23) metal coordination : angle 4.17953 / 2.80 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 125 TYR cc_start: 0.8781 (m-80) cc_final: 0.8276 (t80) REVERT: C 168 LEU cc_start: 0.8723 (mt) cc_final: 0.8425 (mp) REVERT: C 330 GLU cc_start: 0.8702 (mt-10) cc_final: 0.7753 (tm-30) REVERT: C 346 MET cc_start: 0.8810 (tpp) cc_final: 0.8416 (ttm) REVERT: A 88 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8834 (mp10) REVERT: A 110 CYS cc_start: 0.9646 (m) cc_final: 0.9393 (m) REVERT: A 148 MET cc_start: 0.9278 (tpp) cc_final: 0.9042 (tpp) REVERT: A 176 GLU cc_start: 0.9501 (tt0) cc_final: 0.9241 (tm-30) REVERT: A 241 CYS cc_start: 0.9481 (t) cc_final: 0.9148 (p) REVERT: A 390 MET cc_start: 0.9421 (ppp) cc_final: 0.9100 (ppp) REVERT: A 482 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8378 (tp30) REVERT: A 494 MET cc_start: 0.9119 (mmt) cc_final: 0.8295 (mmt) REVERT: A 539 MET cc_start: 0.7144 (pmm) cc_final: 0.6800 (pmm) REVERT: A 704 MET cc_start: 0.8772 (tpt) cc_final: 0.8216 (tpp) REVERT: A 713 ASN cc_start: 0.9331 (m-40) cc_final: 0.9041 (p0) REVERT: A 720 TYR cc_start: 0.8783 (m-10) cc_final: 0.8546 (m-10) REVERT: B 282 MET cc_start: 0.9182 (tpp) cc_final: 0.8910 (tpp) REVERT: B 361 ASP cc_start: 0.9196 (t70) cc_final: 0.8829 (t0) REVERT: B 437 MET cc_start: 0.9347 (ttp) cc_final: 0.8991 (tmm) REVERT: B 581 MET cc_start: 0.9209 (mmm) cc_final: 0.8957 (mmm) REVERT: B 875 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 1036 MET cc_start: 0.9004 (ttp) cc_final: 0.8783 (ttt) REVERT: B 1123 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8222 (tp30) REVERT: D 15 ARG cc_start: 0.9223 (ttm110) cc_final: 0.8827 (ttp-110) REVERT: D 63 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8823 (mtmt) REVERT: D 74 TYR cc_start: 0.8870 (m-10) cc_final: 0.8210 (m-80) REVERT: D 78 ILE cc_start: 0.9085 (mm) cc_final: 0.8752 (mm) REVERT: D 90 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7670 (tpp80) REVERT: N 1 MET cc_start: 0.7815 (ttm) cc_final: 0.7480 (ttp) REVERT: N 40 GLN cc_start: 0.7502 (mt0) cc_final: 0.7105 (mt0) REVERT: N 52 ASP cc_start: 0.9380 (m-30) cc_final: 0.8968 (p0) REVERT: R 33 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.6982 (p90) REVERT: R 47 ASN cc_start: 0.8403 (m-40) cc_final: 0.8091 (m-40) REVERT: R 54 ILE cc_start: 0.9434 (pt) cc_final: 0.9082 (pt) REVERT: R 55 GLU cc_start: 0.9610 (tp30) cc_final: 0.9292 (pt0) REVERT: R 76 ASN cc_start: 0.9279 (t0) cc_final: 0.9054 (m-40) REVERT: R 81 PHE cc_start: 0.9200 (t80) cc_final: 0.8941 (t80) REVERT: R 102 GLU cc_start: 0.9086 (pm20) cc_final: 0.8820 (mp0) REVERT: U 34 GLU cc_start: 0.9252 (tp30) cc_final: 0.8637 (tm-30) REVERT: U 54 ARG cc_start: 0.9273 (mtt-85) cc_final: 0.9052 (mtp85) REVERT: U 72 ARG cc_start: 0.8681 (ttp80) cc_final: 0.7831 (ttm110) outliers start: 45 outliers final: 28 residues processed: 249 average time/residue: 0.1441 time to fit residues: 55.8690 Evaluate side-chains 234 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain N residue 41 GLN Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 26 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [96, 95, 203, 11, 7, 217, 120, 26, 143, 92, 142] chunk 96 optimal weight: 50.0000 chunk 95 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054483 restraints weight = 67819.068| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.35 r_work: 0.2790 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 21176 Z= 0.227 Angle : 0.609 9.389 28630 Z= 0.313 Chirality : 0.043 0.168 3230 Planarity : 0.004 0.046 3669 Dihedral : 6.208 155.203 2830 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.02 % Allowed : 12.82 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.57 (0.17), residues: 2584 helix: 1.80 (0.20), residues: 730 sheet: -0.68 (0.20), residues: 647 loop : -1.61 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 369 TYR 0.017 0.001 TYR B 613 PHE 0.025 0.001 PHE A 397 TRP 0.043 0.002 TRP A 569 HIS 0.005 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (21152) covalent geometry : angle 0.60156 / 0.31 (28612) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 0.52632 / 0.24 ( 2) hydrogen bonds : bond 0.04208 / 2.90 ( 842) hydrogen bonds : angle 4.73984 / 3.30 ( 2409) metal coordination : bond 0.00876 / 0.49 ( 23) metal coordination : angle 4.08202 / 2.74 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 125 TYR cc_start: 0.8765 (m-80) cc_final: 0.8337 (t80) REVERT: C 330 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7775 (tm-30) REVERT: C 342 LEU cc_start: 0.8758 (tp) cc_final: 0.8498 (mt) REVERT: C 346 MET cc_start: 0.8846 (tpp) cc_final: 0.8638 (ttm) REVERT: A 110 CYS cc_start: 0.9654 (m) cc_final: 0.9396 (m) REVERT: A 241 CYS cc_start: 0.9495 (t) cc_final: 0.9137 (p) REVERT: A 390 MET cc_start: 0.9425 (ppp) cc_final: 0.9091 (ppp) REVERT: A 482 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8365 (tp30) REVERT: A 494 MET cc_start: 0.9189 (mmt) cc_final: 0.8288 (mmm) REVERT: A 539 MET cc_start: 0.7042 (pmm) cc_final: 0.6613 (pmm) REVERT: A 704 MET cc_start: 0.8778 (tpt) cc_final: 0.8235 (tpp) REVERT: A 713 ASN cc_start: 0.9359 (m-40) cc_final: 0.9046 (p0) REVERT: B 282 MET cc_start: 0.9117 (tpp) cc_final: 0.8816 (tpp) REVERT: B 361 ASP cc_start: 0.9219 (t70) cc_final: 0.8859 (t0) REVERT: B 437 MET cc_start: 0.9350 (ttp) cc_final: 0.9002 (tmm) REVERT: B 581 MET cc_start: 0.9218 (mmm) cc_final: 0.8949 (mmm) REVERT: B 679 MET cc_start: 0.9126 (tmm) cc_final: 0.8472 (tmm) REVERT: B 875 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8692 (tm-30) REVERT: B 1120 MET cc_start: 0.7777 (mmm) cc_final: 0.7423 (mmm) REVERT: D 15 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8815 (ttp-110) REVERT: D 63 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8713 (mtmt) REVERT: D 74 TYR cc_start: 0.8952 (m-10) cc_final: 0.8457 (m-80) REVERT: D 78 ILE cc_start: 0.9110 (mm) cc_final: 0.8812 (mm) REVERT: N 1 MET cc_start: 0.8088 (ttm) cc_final: 0.7610 (ttp) REVERT: N 28 GLU cc_start: 0.9323 (pt0) cc_final: 0.8894 (pp20) REVERT: N 29 ARG cc_start: 0.9396 (mmm160) cc_final: 0.8965 (mmm160) REVERT: N 31 GLU cc_start: 0.8926 (tp30) cc_final: 0.8694 (mm-30) REVERT: N 40 GLN cc_start: 0.7045 (mt0) cc_final: 0.6695 (mt0) REVERT: R 33 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.6925 (p90) REVERT: R 54 ILE cc_start: 0.9462 (pt) cc_final: 0.9214 (pt) REVERT: R 55 GLU cc_start: 0.9629 (tp30) cc_final: 0.9141 (tm-30) REVERT: R 81 PHE cc_start: 0.9200 (t80) cc_final: 0.8874 (t80) REVERT: R 89 LYS cc_start: 0.9634 (ttmm) cc_final: 0.9312 (mtmm) REVERT: R 102 GLU cc_start: 0.9120 (pm20) cc_final: 0.8846 (mp0) REVERT: U 18 GLU cc_start: 0.8588 (pm20) cc_final: 0.8355 (pm20) REVERT: U 34 GLU cc_start: 0.9310 (tp30) cc_final: 0.8672 (tm-30) REVERT: U 54 ARG cc_start: 0.9374 (mtt-85) cc_final: 0.9006 (mtp85) REVERT: U 72 ARG cc_start: 0.8739 (ttp80) cc_final: 0.7983 (ttm110) outliers start: 46 outliers final: 31 residues processed: 241 average time/residue: 0.1453 time to fit residues: 55.3111 Evaluate side-chains 232 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 26 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [53, 71, 220, 41, 52, 203, 137, 181, 104, 14, 190] chunk 53 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 220 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 203 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.085699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055795 restraints weight = 67191.378| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.33 r_work: 0.2834 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21176 Z= 0.123 Angle : 0.564 10.398 28630 Z= 0.287 Chirality : 0.042 0.161 3230 Planarity : 0.003 0.044 3669 Dihedral : 6.074 153.717 2830 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.54 % Allowed : 14.05 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.48 (0.17), residues: 2584 helix: 1.82 (0.20), residues: 731 sheet: -0.54 (0.20), residues: 643 loop : -1.57 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.019 0.001 TYR A 720 PHE 0.023 0.001 PHE A 397 TRP 0.044 0.002 TRP A 569 HIS 0.004 0.001 HIS R 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21152) covalent geometry : angle 0.55758 / 0.29 (28612) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.61233 / 0.28 ( 2) hydrogen bonds : bond 0.03642 / 2.52 ( 842) hydrogen bonds : angle 4.54787 / 3.15 ( 2409) metal coordination : bond 0.00812 / 0.39 ( 23) metal coordination : angle 3.58012 / 2.42 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8729 (m-80) cc_final: 0.8306 (t80) REVERT: C 330 GLU cc_start: 0.8674 (mt-10) cc_final: 0.7692 (tm-30) REVERT: C 342 LEU cc_start: 0.8730 (tp) cc_final: 0.8474 (mt) REVERT: A 110 CYS cc_start: 0.9640 (m) cc_final: 0.9367 (m) REVERT: A 146 MET cc_start: 0.9239 (tpp) cc_final: 0.8980 (tpp) REVERT: A 241 CYS cc_start: 0.9481 (t) cc_final: 0.9138 (p) REVERT: A 390 MET cc_start: 0.9436 (ppp) cc_final: 0.9091 (ppp) REVERT: A 482 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8335 (tp30) REVERT: A 494 MET cc_start: 0.9131 (mmt) cc_final: 0.8313 (mmt) REVERT: A 539 MET cc_start: 0.7051 (pmm) cc_final: 0.6555 (pmm) REVERT: A 704 MET cc_start: 0.8789 (tpt) cc_final: 0.8237 (tpp) REVERT: A 713 ASN cc_start: 0.9344 (m-40) cc_final: 0.9108 (p0) REVERT: B 282 MET cc_start: 0.9089 (tpp) cc_final: 0.8785 (tpp) REVERT: B 361 ASP cc_start: 0.9178 (t70) cc_final: 0.8845 (t0) REVERT: B 437 MET cc_start: 0.9268 (ttp) cc_final: 0.9062 (tmm) REVERT: B 478 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8312 (tt) REVERT: B 548 ASP cc_start: 0.9373 (p0) cc_final: 0.9076 (t0) REVERT: B 581 MET cc_start: 0.9184 (mmm) cc_final: 0.8932 (mmm) REVERT: B 875 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8719 (tm-30) REVERT: B 1105 MET cc_start: 0.9241 (mtm) cc_final: 0.9017 (mtm) REVERT: D 15 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8811 (ttp-110) REVERT: D 63 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8753 (mtmt) REVERT: D 71 THR cc_start: 0.9656 (m) cc_final: 0.9142 (p) REVERT: D 74 TYR cc_start: 0.9031 (m-10) cc_final: 0.8446 (m-80) REVERT: D 78 ILE cc_start: 0.9066 (mm) cc_final: 0.8786 (mm) REVERT: N 1 MET cc_start: 0.8084 (ttm) cc_final: 0.7618 (ttp) REVERT: N 28 GLU cc_start: 0.9289 (pt0) cc_final: 0.8782 (pp20) REVERT: N 29 ARG cc_start: 0.9407 (mmm160) cc_final: 0.8952 (mmm160) REVERT: N 31 GLU cc_start: 0.9003 (tp30) cc_final: 0.8677 (mm-30) REVERT: N 40 GLN cc_start: 0.7290 (mt0) cc_final: 0.6921 (mt0) REVERT: N 52 ASP cc_start: 0.9539 (m-30) cc_final: 0.9029 (p0) REVERT: N 54 LYS cc_start: 0.8911 (mmtm) cc_final: 0.8484 (mmtm) REVERT: R 33 TRP cc_start: 0.8029 (OUTLIER) cc_final: 0.6843 (p90) REVERT: R 54 ILE cc_start: 0.9434 (pt) cc_final: 0.9115 (pt) REVERT: R 55 GLU cc_start: 0.9611 (tp30) cc_final: 0.9126 (tm-30) REVERT: R 81 PHE cc_start: 0.9171 (t80) cc_final: 0.8919 (t80) REVERT: R 102 GLU cc_start: 0.9080 (pm20) cc_final: 0.8866 (mp0) REVERT: U 18 GLU cc_start: 0.8701 (pm20) cc_final: 0.8489 (pm20) REVERT: U 34 GLU cc_start: 0.9287 (tp30) cc_final: 0.8656 (tm-30) REVERT: U 59 TYR cc_start: 0.9223 (m-10) cc_final: 0.8962 (m-10) REVERT: U 72 ARG cc_start: 0.8735 (ttp80) cc_final: 0.7947 (ttm110) outliers start: 35 outliers final: 28 residues processed: 244 average time/residue: 0.1459 time to fit residues: 55.5687 Evaluate side-chains 230 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 43 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [201, 66, 95, 31, 150, 91, 174, 82, 231, 213, 169] chunk 201 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.084364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054099 restraints weight = 67467.958| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.34 r_work: 0.2735 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 21176 Z= 0.209 Angle : 0.606 10.650 28630 Z= 0.310 Chirality : 0.042 0.170 3230 Planarity : 0.004 0.046 3669 Dihedral : 6.196 155.086 2830 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.46 % Allowed : 13.83 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.58 (0.17), residues: 2584 helix: 1.75 (0.20), residues: 731 sheet: -0.62 (0.21), residues: 640 loop : -1.63 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 369 TYR 0.034 0.001 TYR A 720 PHE 0.021 0.001 PHE A 397 TRP 0.033 0.002 TRP A 569 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (21152) covalent geometry : angle 0.59956 / 0.31 (28612) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.43783 / 0.21 ( 2) hydrogen bonds : bond 0.04083 / 2.81 ( 842) hydrogen bonds : angle 4.63060 / 3.22 ( 2409) metal coordination : bond 0.00755 / 0.43 ( 23) metal coordination : angle 3.83710 / 2.59 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8760 (m-80) cc_final: 0.8400 (t80) REVERT: C 330 GLU cc_start: 0.8729 (mt-10) cc_final: 0.7769 (tm-30) REVERT: A 110 CYS cc_start: 0.9646 (m) cc_final: 0.9394 (m) REVERT: A 241 CYS cc_start: 0.9510 (t) cc_final: 0.9136 (p) REVERT: A 390 MET cc_start: 0.9416 (ppp) cc_final: 0.9069 (ppp) REVERT: A 482 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8336 (tp30) REVERT: A 494 MET cc_start: 0.9127 (mmt) cc_final: 0.8309 (mmt) REVERT: A 539 MET cc_start: 0.6895 (pmm) cc_final: 0.6360 (pmm) REVERT: A 704 MET cc_start: 0.8783 (tpt) cc_final: 0.8331 (tpp) REVERT: A 713 ASN cc_start: 0.9305 (m-40) cc_final: 0.9060 (p0) REVERT: B 209 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: B 282 MET cc_start: 0.9100 (tpp) cc_final: 0.8772 (tpp) REVERT: B 361 ASP cc_start: 0.9194 (t70) cc_final: 0.8841 (t0) REVERT: B 437 MET cc_start: 0.9307 (ttp) cc_final: 0.9018 (tmm) REVERT: B 548 ASP cc_start: 0.9408 (p0) cc_final: 0.9108 (t0) REVERT: B 581 MET cc_start: 0.9226 (mmm) cc_final: 0.8939 (mmm) REVERT: B 679 MET cc_start: 0.9151 (tmm) cc_final: 0.8541 (tmm) REVERT: B 875 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8727 (tm-30) REVERT: B 1036 MET cc_start: 0.9110 (ttp) cc_final: 0.8895 (ttt) REVERT: B 1120 MET cc_start: 0.7896 (mmm) cc_final: 0.7529 (mmm) REVERT: D 15 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8798 (ttp-110) REVERT: D 74 TYR cc_start: 0.9029 (m-10) cc_final: 0.8578 (m-80) REVERT: N 1 MET cc_start: 0.8211 (ttm) cc_final: 0.7722 (ttp) REVERT: N 28 GLU cc_start: 0.9343 (pt0) cc_final: 0.8874 (pp20) REVERT: N 29 ARG cc_start: 0.9426 (mmm160) cc_final: 0.8930 (mmm160) REVERT: N 31 GLU cc_start: 0.9000 (tp30) cc_final: 0.8683 (mm-30) REVERT: N 40 GLN cc_start: 0.7697 (mt0) cc_final: 0.7259 (mt0) REVERT: N 50 MET cc_start: 0.8666 (mmm) cc_final: 0.8213 (mmm) REVERT: N 52 ASP cc_start: 0.9558 (m-30) cc_final: 0.9069 (p0) REVERT: N 54 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8412 (mmtm) REVERT: R 33 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.6979 (p90) REVERT: R 54 ILE cc_start: 0.9422 (pt) cc_final: 0.9169 (pt) REVERT: R 55 GLU cc_start: 0.9620 (tp30) cc_final: 0.9118 (tm-30) REVERT: R 81 PHE cc_start: 0.9227 (t80) cc_final: 0.8886 (t80) REVERT: R 89 LYS cc_start: 0.9654 (ttmm) cc_final: 0.9331 (mtmm) REVERT: R 91 ARG cc_start: 0.8403 (tmm-80) cc_final: 0.8193 (tmm-80) REVERT: R 102 GLU cc_start: 0.9139 (pm20) cc_final: 0.8834 (mp0) REVERT: U 18 GLU cc_start: 0.8766 (pm20) cc_final: 0.8363 (pm20) REVERT: U 21 ASP cc_start: 0.9178 (m-30) cc_final: 0.8281 (m-30) REVERT: U 34 GLU cc_start: 0.9331 (tp30) cc_final: 0.8687 (tm-30) REVERT: U 54 ARG cc_start: 0.9330 (mtt-85) cc_final: 0.9006 (mtp85) REVERT: U 72 ARG cc_start: 0.8707 (ttp80) cc_final: 0.7934 (ttm110) outliers start: 56 outliers final: 40 residues processed: 242 average time/residue: 0.1439 time to fit residues: 54.6749 Evaluate side-chains 236 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain U residue 9 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 43 LEU Chi-restraints excluded: chain U residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [227, 98, 7, 121, 9, 35, 208, 57, 1, 56, 60] chunk 227 optimal weight: 0.3980 chunk 98 optimal weight: 30.0000 chunk 7 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.086061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055970 restraints weight = 67333.019| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.36 r_work: 0.2829 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21176 Z= 0.109 Angle : 0.575 11.242 28630 Z= 0.289 Chirality : 0.042 0.165 3230 Planarity : 0.003 0.043 3669 Dihedral : 6.020 154.186 2830 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.45 % Allowed : 15.11 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.47 (0.17), residues: 2584 helix: 1.84 (0.20), residues: 731 sheet: -0.52 (0.20), residues: 646 loop : -1.58 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 369 TYR 0.018 0.001 TYR A 720 PHE 0.053 0.001 PHE C 150 TRP 0.021 0.001 TRP A 569 HIS 0.004 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21152) covalent geometry : angle 0.56961 / 0.29 (28612) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 0.63950 / 0.30 ( 2) hydrogen bonds : bond 0.03366 / 2.33 ( 842) hydrogen bonds : angle 4.41369 / 3.08 ( 2409) metal coordination : bond 0.00845 / 0.39 ( 23) metal coordination : angle 3.32359 / 2.26 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8720 (m-80) cc_final: 0.8217 (t80) REVERT: C 150 PHE cc_start: 0.8705 (t80) cc_final: 0.8431 (t80) REVERT: C 330 GLU cc_start: 0.8663 (mt-10) cc_final: 0.7678 (tm-30) REVERT: C 342 LEU cc_start: 0.8709 (tp) cc_final: 0.8458 (mt) REVERT: A 110 CYS cc_start: 0.9638 (m) cc_final: 0.9383 (m) REVERT: A 241 CYS cc_start: 0.9489 (t) cc_final: 0.9121 (p) REVERT: A 390 MET cc_start: 0.9434 (ppp) cc_final: 0.9085 (ppp) REVERT: A 482 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8309 (tp30) REVERT: A 494 MET cc_start: 0.9067 (mmt) cc_final: 0.8272 (mmt) REVERT: A 539 MET cc_start: 0.6972 (pmm) cc_final: 0.6408 (pmm) REVERT: A 704 MET cc_start: 0.8779 (tpt) cc_final: 0.8387 (tpt) REVERT: A 713 ASN cc_start: 0.9311 (m-40) cc_final: 0.9090 (p0) REVERT: B 209 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B 282 MET cc_start: 0.9061 (tpp) cc_final: 0.8739 (tpp) REVERT: B 361 ASP cc_start: 0.9171 (t70) cc_final: 0.8853 (t0) REVERT: B 437 MET cc_start: 0.9291 (ttp) cc_final: 0.9071 (tmm) REVERT: B 548 ASP cc_start: 0.9393 (p0) cc_final: 0.9088 (t0) REVERT: B 581 MET cc_start: 0.9233 (mmm) cc_final: 0.8934 (mmm) REVERT: B 875 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8711 (tm-30) REVERT: B 1120 MET cc_start: 0.7886 (mmm) cc_final: 0.7523 (mmm) REVERT: D 15 ARG cc_start: 0.9226 (ttm110) cc_final: 0.8831 (ttp-110) REVERT: D 74 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: D 140 GLU cc_start: 0.9503 (mm-30) cc_final: 0.9300 (mp0) REVERT: D 144 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8772 (ptpp) REVERT: N 1 MET cc_start: 0.8374 (ttm) cc_final: 0.7847 (ttp) REVERT: N 28 GLU cc_start: 0.9313 (pt0) cc_final: 0.8845 (pp20) REVERT: N 29 ARG cc_start: 0.9400 (mmm160) cc_final: 0.8953 (mmm160) REVERT: N 31 GLU cc_start: 0.9005 (tp30) cc_final: 0.8667 (mm-30) REVERT: N 40 GLN cc_start: 0.7459 (mt0) cc_final: 0.6998 (mt0) REVERT: N 50 MET cc_start: 0.8638 (mmm) cc_final: 0.8252 (mmm) REVERT: N 52 ASP cc_start: 0.9547 (m-30) cc_final: 0.9035 (p0) REVERT: N 54 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8338 (mmtm) REVERT: R 33 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7054 (p90) REVERT: R 47 ASN cc_start: 0.8432 (m-40) cc_final: 0.8140 (m-40) REVERT: R 54 ILE cc_start: 0.9405 (pt) cc_final: 0.9052 (pt) REVERT: R 55 GLU cc_start: 0.9630 (tp30) cc_final: 0.9145 (tm-30) REVERT: R 81 PHE cc_start: 0.9199 (t80) cc_final: 0.8953 (t80) REVERT: R 102 GLU cc_start: 0.9105 (pm20) cc_final: 0.8777 (mp0) REVERT: U 18 GLU cc_start: 0.8736 (pm20) cc_final: 0.8496 (pm20) REVERT: U 21 ASP cc_start: 0.9205 (m-30) cc_final: 0.8506 (m-30) REVERT: U 34 GLU cc_start: 0.9323 (tp30) cc_final: 0.8699 (tm-30) REVERT: U 59 TYR cc_start: 0.9244 (m-10) cc_final: 0.8991 (m-10) REVERT: U 72 ARG cc_start: 0.8726 (ttp80) cc_final: 0.7957 (ttm110) outliers start: 33 outliers final: 20 residues processed: 237 average time/residue: 0.1460 time to fit residues: 53.8311 Evaluate side-chains 222 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain U residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [81, 201, 121, 22, 100, 28, 192, 90, 233, 126, 218] chunk 81 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 0.0040 chunk 22 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 192 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057234 restraints weight = 66001.379| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.30 r_work: 0.2856 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21176 Z= 0.101 Angle : 0.573 12.025 28630 Z= 0.287 Chirality : 0.042 0.188 3230 Planarity : 0.003 0.070 3669 Dihedral : 5.929 154.421 2830 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.27 % Allowed : 15.28 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.42 (0.17), residues: 2584 helix: 1.82 (0.20), residues: 730 sheet: -0.44 (0.20), residues: 647 loop : -1.54 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.042 0.001 TYR A 720 PHE 0.049 0.001 PHE C 150 TRP 0.016 0.001 TRP R 33 HIS 0.004 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (21152) covalent geometry : angle 0.56833 / 0.29 (28612) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.53660 / 0.25 ( 2) hydrogen bonds : bond 0.03101 / 2.15 ( 842) hydrogen bonds : angle 4.30360 / 3.01 ( 2409) metal coordination : bond 0.00868 / 0.42 ( 23) metal coordination : angle 3.11042 / 2.12 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8699 (m-80) cc_final: 0.8123 (t80) REVERT: C 194 MET cc_start: 0.9336 (tpp) cc_final: 0.9079 (mmm) REVERT: C 330 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7682 (tm-30) REVERT: C 342 LEU cc_start: 0.8712 (tp) cc_final: 0.8447 (mt) REVERT: A 110 CYS cc_start: 0.9625 (m) cc_final: 0.9369 (m) REVERT: A 148 MET cc_start: 0.9271 (tpp) cc_final: 0.9045 (tpp) REVERT: A 241 CYS cc_start: 0.9460 (t) cc_final: 0.9105 (p) REVERT: A 390 MET cc_start: 0.9439 (ppp) cc_final: 0.9080 (ppp) REVERT: A 456 ASP cc_start: 0.9038 (p0) cc_final: 0.8832 (p0) REVERT: A 482 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8259 (tp30) REVERT: A 494 MET cc_start: 0.9065 (mmt) cc_final: 0.8300 (mmt) REVERT: A 539 MET cc_start: 0.6944 (pmm) cc_final: 0.6335 (pmm) REVERT: A 704 MET cc_start: 0.8720 (tpt) cc_final: 0.8323 (tpt) REVERT: A 713 ASN cc_start: 0.9307 (m-40) cc_final: 0.9070 (p0) REVERT: B 209 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: B 282 MET cc_start: 0.9052 (tpp) cc_final: 0.8764 (tpp) REVERT: B 361 ASP cc_start: 0.9097 (t70) cc_final: 0.8848 (t0) REVERT: B 437 MET cc_start: 0.9310 (ttp) cc_final: 0.9094 (tmm) REVERT: B 548 ASP cc_start: 0.9359 (p0) cc_final: 0.9052 (t0) REVERT: B 581 MET cc_start: 0.9231 (mmm) cc_final: 0.8951 (mmm) REVERT: B 875 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8654 (tm-30) REVERT: D 15 ARG cc_start: 0.9214 (ttm110) cc_final: 0.8902 (ttp-110) REVERT: D 63 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8814 (mtmt) REVERT: D 74 TYR cc_start: 0.8934 (m-10) cc_final: 0.8443 (m-80) REVERT: D 78 ILE cc_start: 0.8922 (mm) cc_final: 0.8573 (mm) REVERT: N 1 MET cc_start: 0.8282 (ttm) cc_final: 0.7755 (ttp) REVERT: N 28 GLU cc_start: 0.9307 (pt0) cc_final: 0.8826 (pp20) REVERT: N 29 ARG cc_start: 0.9379 (mmm160) cc_final: 0.8959 (mmm160) REVERT: N 31 GLU cc_start: 0.9048 (tp30) cc_final: 0.8742 (mm-30) REVERT: N 40 GLN cc_start: 0.7420 (mt0) cc_final: 0.7141 (mt0) REVERT: N 50 MET cc_start: 0.8653 (mmm) cc_final: 0.8370 (mmm) REVERT: N 52 ASP cc_start: 0.9544 (m-30) cc_final: 0.9037 (p0) REVERT: N 54 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8326 (mmtm) REVERT: R 33 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.6937 (p90) REVERT: R 47 ASN cc_start: 0.8415 (m-40) cc_final: 0.8134 (m-40) REVERT: R 54 ILE cc_start: 0.9391 (pt) cc_final: 0.9030 (pt) REVERT: R 55 GLU cc_start: 0.9616 (tp30) cc_final: 0.9129 (tm-30) REVERT: R 81 PHE cc_start: 0.9193 (t80) cc_final: 0.8944 (t80) REVERT: R 102 GLU cc_start: 0.9090 (pm20) cc_final: 0.8767 (mp0) REVERT: U 18 GLU cc_start: 0.8709 (pm20) cc_final: 0.8478 (pm20) REVERT: U 21 ASP cc_start: 0.9160 (m-30) cc_final: 0.8407 (m-30) REVERT: U 34 GLU cc_start: 0.9313 (tp30) cc_final: 0.8695 (tm-30) REVERT: U 59 TYR cc_start: 0.9246 (m-10) cc_final: 0.9005 (m-10) REVERT: U 72 ARG cc_start: 0.8731 (ttp80) cc_final: 0.7987 (ttm110) outliers start: 29 outliers final: 21 residues processed: 237 average time/residue: 0.1415 time to fit residues: 52.6681 Evaluate side-chains 225 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 1112 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain U residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [52, 133, 198, 249, 197, 20, 132, 148, 123, 55, 237] chunk 52 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 0.2980 chunk 249 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.4196 > 50:) chunk 148 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 237 optimal weight: 0.4980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056281 restraints weight = 67678.555| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.38 r_work: 0.2839 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21176 Z= 0.118 Angle : 0.597 12.207 28630 Z= 0.298 Chirality : 0.042 0.300 3230 Planarity : 0.003 0.044 3669 Dihedral : 5.929 154.320 2830 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.27 % Allowed : 15.90 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.38 (0.17), residues: 2584 helix: 1.83 (0.20), residues: 730 sheet: -0.42 (0.20), residues: 646 loop : -1.50 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.014 0.001 TYR A 720 PHE 0.019 0.001 PHE A 554 TRP 0.026 0.001 TRP D 141 HIS 0.003 0.001 HIS R 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21152) covalent geometry : angle 0.59241 / 0.30 (28612) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.44344 / 0.20 ( 2) hydrogen bonds : bond 0.03223 / 2.22 ( 842) hydrogen bonds : angle 4.32255 / 3.03 ( 2409) metal coordination : bond 0.00798 / 0.38 ( 23) metal coordination : angle 3.16946 / 2.15 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 TYR cc_start: 0.8694 (m-80) cc_final: 0.8142 (t80) REVERT: C 194 MET cc_start: 0.9369 (tpp) cc_final: 0.9103 (mmm) REVERT: C 330 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7694 (tm-30) REVERT: A 110 CYS cc_start: 0.9630 (m) cc_final: 0.9375 (m) REVERT: A 148 MET cc_start: 0.9287 (tpp) cc_final: 0.9066 (tpp) REVERT: A 241 CYS cc_start: 0.9480 (t) cc_final: 0.9113 (p) REVERT: A 390 MET cc_start: 0.9439 (ppp) cc_final: 0.9076 (ppp) REVERT: A 482 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8285 (tp30) REVERT: A 494 MET cc_start: 0.9031 (mmt) cc_final: 0.8380 (mmt) REVERT: A 539 MET cc_start: 0.6993 (pmm) cc_final: 0.6361 (pmm) REVERT: A 704 MET cc_start: 0.8673 (tpt) cc_final: 0.8277 (tpt) REVERT: A 713 ASN cc_start: 0.9297 (m-40) cc_final: 0.9057 (p0) REVERT: B 209 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8237 (tm-30) REVERT: B 282 MET cc_start: 0.9054 (tpp) cc_final: 0.8746 (tpp) REVERT: B 361 ASP cc_start: 0.9126 (t70) cc_final: 0.8867 (t0) REVERT: B 437 MET cc_start: 0.9301 (ttp) cc_final: 0.9092 (tmm) REVERT: B 548 ASP cc_start: 0.9376 (p0) cc_final: 0.9082 (t0) REVERT: B 581 MET cc_start: 0.9235 (mmm) cc_final: 0.8957 (mmm) REVERT: B 875 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 1120 MET cc_start: 0.8217 (mmm) cc_final: 0.7554 (mmp) REVERT: D 15 ARG cc_start: 0.9238 (ttm110) cc_final: 0.8919 (ttm110) REVERT: D 63 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8805 (mtmt) REVERT: D 74 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8420 (m-80) REVERT: D 78 ILE cc_start: 0.8909 (mm) cc_final: 0.8574 (mm) REVERT: D 140 GLU cc_start: 0.9507 (mp0) cc_final: 0.9283 (pm20) REVERT: N 1 MET cc_start: 0.8329 (ttm) cc_final: 0.7831 (ttp) REVERT: N 28 GLU cc_start: 0.9272 (pt0) cc_final: 0.8757 (pp20) REVERT: N 29 ARG cc_start: 0.9379 (mmm160) cc_final: 0.8943 (mmm160) REVERT: N 31 GLU cc_start: 0.9029 (tp30) cc_final: 0.8741 (mm-30) REVERT: N 40 GLN cc_start: 0.7436 (mt0) cc_final: 0.7160 (mt0) REVERT: N 50 MET cc_start: 0.8671 (mmm) cc_final: 0.8346 (mmm) REVERT: N 52 ASP cc_start: 0.9546 (m-30) cc_final: 0.9044 (p0) REVERT: N 54 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8331 (mmtm) REVERT: R 33 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7138 (p90) REVERT: R 47 ASN cc_start: 0.8376 (m-40) cc_final: 0.8075 (m-40) REVERT: R 54 ILE cc_start: 0.9387 (pt) cc_final: 0.9023 (pt) REVERT: R 55 GLU cc_start: 0.9621 (tp30) cc_final: 0.9138 (tm-30) REVERT: R 81 PHE cc_start: 0.9206 (t80) cc_final: 0.8942 (t80) REVERT: R 102 GLU cc_start: 0.9115 (pm20) cc_final: 0.8786 (mp0) REVERT: U 2 GLN cc_start: 0.9033 (pm20) cc_final: 0.8533 (pp30) REVERT: U 18 GLU cc_start: 0.8753 (pm20) cc_final: 0.8523 (pm20) REVERT: U 21 ASP cc_start: 0.9160 (m-30) cc_final: 0.8402 (m-30) REVERT: U 34 GLU cc_start: 0.9320 (tp30) cc_final: 0.8703 (tm-30) REVERT: U 59 TYR cc_start: 0.9253 (m-10) cc_final: 0.9009 (m-10) REVERT: U 72 ARG cc_start: 0.8747 (ttp80) cc_final: 0.7993 (ttm110) outliers start: 29 outliers final: 22 residues processed: 227 average time/residue: 0.1403 time to fit residues: 50.3887 Evaluate side-chains 227 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 74 TYR Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain U residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: [252, 170, 138, 43, 200, 62, 102, 7, 33, 152, 172] chunk 252 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 172 optimal weight: 0.1980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054949 restraints weight = 67992.832| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.32 r_work: 0.2801 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21176 Z= 0.178 Angle : 0.617 11.762 28630 Z= 0.312 Chirality : 0.042 0.293 3230 Planarity : 0.004 0.045 3669 Dihedral : 6.027 154.846 2830 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.32 % Allowed : 15.81 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 are not related in a simple way. whole: -0.45 (0.17), residues: 2584 helix: 1.80 (0.20), residues: 732 sheet: -0.50 (0.21), residues: 638 loop : -1.53 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.014 0.001 TYR B 613 PHE 0.020 0.001 PHE U 45 TRP 0.026 0.002 TRP D 141 HIS 0.004 0.001 HIS I 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (21152) covalent geometry : angle 0.61156 / 0.31 (28612) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.33848 / 0.17 ( 2) hydrogen bonds : bond 0.03643 / 2.50 ( 842) hydrogen bonds : angle 4.43107 / 3.10 ( 2409) metal coordination : bond 0.00722 / 0.37 ( 23) metal coordination : angle 3.39877 / 2.32 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5695.51 seconds wall clock time: 97 minutes 53.74 seconds (5873.74 seconds total)